Management of Use Cases

	<program name="boxshade" description="Alignment PrettyPrinter yielding PostScript"
		command="boxshade -def -pep -in=alignment.aln -out=postscript.eps -dev=2">
		<icon url="http://www.ch.embnet.org/favicon.ico" />
		<group name="Alignment" />
		<input name="Multiple_Sequence_Alignment_as_MSF">
			<file path="alignment.aln" />
		</input>
		<output name="PostScript_file">
			<fromfile path="postscript.eps" />
			<mime type="text/plain" />
			<mime type="application/postscript" />
		</output>
		<RE name="APPS/BIO/BOXSHADE-3.3.1-4" relation=">=" />
		<test local="test -x /usr/bin/boxshade" />
	</program>

	<program name="t_coffee" description="call t_coffee"
		command="mkdir .t_coffee ; t_coffee -infile input -outfile output">
		<group name="Alignment" />
		<input name="multiple_sequences_FASTA">
			<file path="input" />
		</input>
		<output name="alignment">
			<fromfile path="output" />
		</output>
		<RE name="APPS/BIO/TCOFFEE-2.5" />
		<test local="/usr/bin/t_coffee" />
	</program>

	<program name="hmmbuild"
		description="Preparation of a Hidden Markov Model from a sequence alignment"
		command="hmmbuild hmmfile alignment.msf">
		<group name="Alignment:HMMER" />
		<input name="Multiple_Sequence_Alignment_as_MSF">
			<file path="alignment.msf" />
		</input>
		<output name="HMM">
			<fromfile path="hmmfile" />
		</output>
		<RE name="APPS/BIO/HMMER-2.3.2" />
		<test local="/usr/bin/hmmbuild" />
	</program>

	<program name="hmmcalibrate" description="Calibration of HMM"
		command="hmmcalibrate hmmfile">
		<group name="Alignment:HMMER" />
		<input name="HMM in demand of calibration">
			<file path="hmmfile" />
		</input>
		<output name="Calibrated HMM">
			<fromfile path="hmmfile" />
		</output>
		<RE name="APPS/BIO/HMMER-2.3.2" />
		<test local="test -x /usr/bin/hmmcalibrate" />
	</program>

	<program name="hmmsearch" description="Search with HMM in Sequence database"
		command="hmmcalibrate hmmfile">
		<group name="Alignment:HMMER" />
		<input name="HMM in demand of calibration">
			<file path="hmmfile" />
		</input>
		<output name="Calibrated HMM">
			<fromfile path="hmmfile" />
		</output>
		<RE name="APPS/BIO/HMMER-2.3.2" />
		<test local="test -x /usr/bin/hmmcalibrate" />
	</program>

	<program name="bourne_shell_script" description="execute shell script"
		command="/bin/sh input">
		<input name="shell script">
			<file path="input" />
		</input>
		<test local="test -x /bin/sh" />
	</program>

	<program name="cmbuild"
		description="Preparation of model for RNA structure with Infernal"
		command="cmbuild cmfile alignment">
		<group name="Alignment:Infernal" />
		<input name="RNA sequence alignment">
			<file path="alignment" />
		</input>
		<output name="Infernal s representation of RNA structure">
			<fromfile path="cmfile" />
		</output>
		<RE name="APPS/BIO/INFERNAL-0.8.1" />
	</program>

<program name="clustalw_protein" description="call clustalw"
      command="clustalw -infile=input -outfile=output">
    <icon url="http://www.ebi.ac.uk/favicon.ico" />
  <group name="Alignment" />
  <input name="multiple_sequences_FASTA">
    <file path="input" />
  </input>
  <output name="alignment">
    <fromfile path="output" />
  </output>
  <RE name="APPS/BIO/CLUSTALW-1.8.3" />
  <test local="test -x /usr/bin/clustalw" />
</program>

<program name="weka_tree_learn" description="creates tree model"
      command="java -mx1024m weka.classifiers.trees.J48 -t data.arff -i -k -d J48-data.model">
 <input name="arff">
  <file path="data.arff" />
 </input>
 <output name="model">
  <fromfile path="J48-data.model" />
 </output>
 <RE name="APPS/BIO/WEKA-3.4.10" />
</program>

<program name="mustang_2" description="Protein Structure Alignment"
	command="mustang -i first.pdb second.pdb -F msf -s ON -o output">
	<group name="Alignment" />
	<input name="pdb_structure_one">
		<file path="first.pdb" />
	</input>
	<input name="pdb_structure_two">
		<file path="second.pdb" />
	</input>
	<output name="combined_structures">
		<fromfile path="output.pdb" />
	</output>
	<output name="structure_derived_alignment">
		<fromfile path="output.msf" />
	</output>
	<RE name="APPS/BIO/MUSTANG-3.0" relation=">=" />
	<test local="test -x /usr/bin/mustang" />
</program>

	<program name="list_input_test" description="test" command="cat %%listfile%%">
		<input name="images" list="true" concatenate="true" binary="true">
			<tempfile tag="listfile" />
		</input>
	</program>

<program name="sift_extraction" description="Run sift extraction"
      command="java -Djava.awt.headless=true -Xms32m -Xmx512m -jar sift.jar %%imagelist%% %%uniqueID%%">
	<group name="Medical Imaging" />
	<input name="jar" binary="true">
		<file path="sift.jar" />
	</input>
	<input name="images" list="true" binary="true">
		<tempfile tag="imagelist" />
	</input>
	<output name="ftsTable">
		<fromfile path="ftsTable.csv" />
	</output>
	<output name="dscpTable">
		<fromfile path="dscpTable.csv" />
	</output>
	<RE name="ENV/JAVA/JRE-1.5.0" />
</program>

<program name="mustang" description="structural alignment of multiple proteins"
	command="mustang -i %%spaceseparatedlistoffiles%% -F msf -s ON -o output">
	<group name="Alignment" />
	<input name="pdb_structures" list="true" concatenate="false"
		binary="false">
		<replace tag="spaceseparatedlistoffiles" />
	</input>
	<output name="combined_structures">
		<fromfile path="output.pdb" />
		<mime type="text/plain" />
		<mime type="chemical/x-pdb" />
	</output>
	<output name="structure_derived_alignment">
		<fromfile path="output.msf" />
		<mime type="text/plain" />
	</output>
	<RE name="APPS/BIO/MUSTANG-3.0" relation=">=" />
	<test local="test -x /usr/bin/mustang" />
</program>

<program name="autodock4" description="docks ligand to fixed-backbone receptor"
	command="sh executeme.sh">
	<icon url="http://autodock.scripps.edu/favicon.ico" />
	<group name="Structure" />
	<input name="Parameters" binary="false">
		<file path="prot.dpf" />
	</input>
	<input name="Macromolecule" binary="false">
		<file path="prot.pdbqt" />
	</input>
	<input name="Ligand" binary="false">
		<file path="prot.dpf" />
	</input>
	<input name="all_created_files_tared_up_for_docking" binary="true">
		<file path="all_files_tared_up_for_docking.tgz" />
	</input>
	<input name="Grid_Maps" list="true" concatenate="false" binary="false">
		<replace tag="spaceseparatedlistoffiles" />
	</input>
	<output name="Log" binary="false">
		<fromfile path="log.dlg" />
	</output>
	<RE name="APPS/BIO/AUTODOCK-4" relation=">=" />
	<static>
		<file path="executeme.sh" />
<content>
tar xzvf all_files_tared_up_for_docking.tgz
autodock4 -p
prot.dpf -l log.dlg
</content>
	</static>
	<test local="test -x /usr/bin/autodock4" />
</program>

<program name="merge_and_kmeans" description="merge_and_kmeans"
      command="java -Djava.awt.headless=true -Xms32m -Xmx512m -jar kmeans.jar %%featurefilelist%%">
  <group name="Medical Imaging" />
  <input name="jar" binary="true">
	<file path="kmeans.jar" />
  </input>
  <input name="dscpTable_files" list="true">
	<tempfile tag="featurefilelist" />
  </input>
  <output name="clustersFile">
	<fromfile path="clustersFile" />
  </output>
  <output name="clstIndexFile">
	<fromfile path="clstIndexFile" />
  </output>
  <output name="dscpTable_merged">
	<fromfile path="dscpTable" />
  </output>
  <output name="dscpTable_map">
	<fromfile path="dscpTableMap" />
  </output>
</program>

<program name="upload_tar_return" description="upload_tar_return"
	command="tar cvf out.tar in">
	<input name="in" binary="true">
		<file path="in" />
	</input>
	<output name="orig" binary="true">
		<fromfile path="in" />
	</output>
	<output name="tar" binary="true">
		<fromfile path="out.tar" />
	</output>
</program>

<program name="autogrid4"
      command="sed -i -e 's/^receptor.*/receptor receptor.pdbqt/' ;
               autogrid4 -p prot.gpf -l log.dlg ;
               tar czvf all_files_tared_up_for_docking.tgz *.map *.fld *.xyz"
  description="Precalculations for a docking experiment.">
 <icon url="http://autodock.scripps.edu/favicon.ico" />
 <group name="Structure" />
 <input name="Dock_Parameter_File" binary="false">
   <file path="prot.dpf" />
 </input>
 <input name="Grid_Parameter_File" binary="false">
   <file path="prot.gpf" />
 </input>
 <input name="AD4_paramters_dat" binary="false">
  <file path="AD4_parameters.dat" />
 </input>
 <input name="Macromolecule_pdbqt" binary="false">
  <file path="receptor.pdbqt" />
 </input>
 <output name="Logfile" binary="false">
  <fromfile path="log.glg" />
 </output>
 <output name="Receptor_unchanged" binary="false">
  <fromfile path="receptor.pdbqt" />
 </output>
 <output name="all_created_files_tared_up_for_docking" binary="true">
  <fromfile path="all_files_tared_up_for_docking.tgz" />
 </output>
 <RE name="APPS/BIO/AUTOGRID-4" relation=">=" />
 <test local="test -x /usr/bin/autogrid4" />
</program>

	<program name="charcounter" description="simple test"
		command="java -jar charcounter.jar inputfile">
		<input name="jar" binary="true">
			<file path="charcounter.jar" />
		</input>
		<input name="countme">
			<file path="inputfile" />
		</input>
	</program>

	<program name="testR" description="cont images" command="java tryRun /etc">
		<input name="classFile" binary="true">
			<file path="tryRun.class" />
		</input>
	</program>

<program name="HelloWorld" description="interprets an internally delivered script"
      command="/bin/sh script.sh">
  <group name="Testing" />
  <static>
<file path="script.sh" />
<content>
echo Hello World!
</content>
  </static>
</program>

	<program name="hostname"
		description="long hostname of machine executing the workflow element"
		command="hostname -f">
		<group name="Testing" />
	</program>

<program name="add" description="adding two numbers"
	command="sh addthem.sh number1.txt number2.txt">
	<group name="Testing" />
	<input name="First number">
		<file path="number1.txt" />
	</input>
	<input name="Second number">
		<file path="number2.txt" />
	</input>
	<RE name="APPS/BIO/MUSTANG-3.0" relation=">=" />
	<static>
		<file path="addthem.sh" />
<content>
if [ ! -r "$1" ]; then
        echo "Cannot read file indicated by first argument '$1'." ;
        exit -1 ;
fi ;

if [ ! -r "$2" ];then
   echo "Cannot read file indicated by second argument '$1'." ;
   exit -1 ;
fi ;

if [ ! -x /usr/bin/bc ]; then
   echo "The bc tool is not installed as /usr/bin/bc, if installed at all." ;
   exit -1 ;
fi ;

a=$(cat $1|tr -d '\n') ;
b=$(cat $2|tr -d '\n') ;
echo "$a+$b" | bc | tr -d '\n'
  
</content>
		</static>
	</program>

	<program name="ps2pdf" description="Convert a Postscript text to binary PDF"
		command="ps2pdf input.ps output.pdf">
		<icon url="http://www.ebi.ac.uk/favicon.ico" />
		<input name="postscript">
			<file path="input.ps" />
			<mime type="text/plain" />
			<mime type="application/postscript" />
		</input>
		<output name="pdf" binary="true">
			<fromfile path="output.pdf" />
			<mime type="application/pdf" />
		</output>
		<RE name="APPS/BIO/CLUSTALW-1.8.3" />
		<test local="test -x /usr/bin/clustalw" />
	</program>

<program name="cat"
	description="concatenation of two streams"
	command="cat file1.txt file2.txt">
	<group name="Testing" />
	<input name="First file">
		<file path="file1.txt" />
	</input>
	<input name="Second file">
		<file path="file2.txt" />
	</input>
</program>

<program name="g_luck"
	description="Quote from Gromacs"
	command="g_luck">
	<group name="GROMACS" />
</program>

<program name="pdb2gmx_gro_top"
	description="Conversion of PDB entry to gromacs format"
	command="sh executeme.sh">
   <group name="GROMACS" />
   <input name="PDB entry">
      <file path="protein.pdb" />
   </input>
  <static>
    <file path="executeme.sh" />
<content>
set -e
pdb2gmx -f protein.pdb -o protein.gro -p protein.top -water spc -ff gromos43a2 -ignh ;
touch topology_include_files.itp ;
tar czf topology_include_files.tar.gz *.itp
</content>
  </static>
  <output name="GROMACS gro protein">
      <fromfile path="protein.gro" />
  </output>
  <output name="GROMACS top topology">
      <fromfile path="protein.top" />
  </output>
  <output name="GROMACS itp topology_include_files tgz">
      <fromfile path="topology_include_files.tar.gz" />
  </output>
</program>

<program name="gro2pdb"
	description="Using GROMACS tool editconf to convert GROMACS .gro file to PDB format"
	command="tar xzf topology_include_files.tgz ; editconf -f protein.gro -o protein.pdb">
   <group name="GROMACS" />
  <input name="GROMACS gro protein">
      <file path="protein.gro" />
  </input>
  <input name="GROMACS top topology">
      <file path="protein.top" />
  </input>
  <input name="GROMACS itp topology include files tgz" binary="true">
      <file path="topology_include_files.tgz" />
  </input>
   <output name="PDB entry">
      <fromfile path="protein.pdb" />
      <mime type="chemical/x-pdb" />
      <mime type="text/plain" />
   </output>
</program>

<program name="grompp"
  description="Using GROMACS tool to prepare md run"
      command="tar xzf topology_include_files.tgz ; grompp -v -f minim.mdp -c protein.gro -p protein.top -o protein.tpr">
   <group name="GROMACS" />
   <output name="GROMACS tpr file">
      <fromfile path="protein.tpr" />
   </output>
   <output name="GROMACS mdp file">
      <fromfile path="mdout.mdp" />
   </output>
   <input name="GROMACS gro protein">
      <file path="protein.gro" />
   </input>
   <input name="GROMACS top topology">
      <file path="protein.top" />
   </input>
   <input name="GROMACS itp topology include files tgz" binary="true">
      <file path="topology_include_files.tgz" />
   </input>
   <input name="GROMACS mdp file">
      <file path="minim.mdp" />
   </input>
</program>

<program name="mdrun"
         description="Using GROMACS tool to run molecular dynamics"
         command="tar xzf topology_include_files.tgz ; mdrun -v -deffnm protein -c protein_last_step.gro">
   <group name="GROMACS" />
   <input name="GROMACS tpr file">
      <file path="protein.tpr" />
   </input>
  <input name="GROMACS gro protein">
      <file path="protein.gro" />
  </input>
  <output name="GROMACS gro protein with last step">
      <fromfile path="protein_last_step.gro" />
  </output>
   <input name="GROMACS top topology">
      <file path="protein.top" />
   </input>
  <input name="GROMACS itp topology include files tgz" binary="true">
      <file path="topology_include_files.tgz" />
  </input>
   <input name="GROMACS mdp file">
      <file path="minim.mdp" />
   </input>
  <output name="GROMACS trr trajectory file">
      <fromfile path="protein.trr" />
  </output>
  <output name="GROMACS log log file">
      <fromfile path="protein.log" />
   </output>
  <output name="GROMACS edr file">
      <fromfile path="protein.edr" />
  </output>
</program>

<program name="gzip"
  description="Compressing single file to STDOUT"
      command="gzip -c fred > fred.gz">
<group name="system" />
<input name="file to compress" binary="true">
 <file path="fred" />
</input>
<output name="gzipped file" binary="true">
 <fromfile path="fred.gz" />
</output>
</program>

<program name="gunzip"
  description="Uncompressing single file to STDOUT"
      command="gunzip -c fred.gz > fred">
<group name="system" />
<input name="gzipped file" binary="true">
 <file path="fred.gz" />
</input>
<output name="decompressed file" binary="true">
 <fromfile path="fred" />
</output>
</program>

<program name="diff"
  description="UNIX tool diff wrapper for differences between two text files"
     command="diff -u from.txt to.txt">
 <input name="original_file">
  <file path="from.txt" />
 </input>
 <input name="modified_file">
  <file path="to.txt" />
 </input>
</program>

<program name="diff_works"
  description="UNIX tool diff wrapper for differences between two text files"
     command="diff -u from.txt to.txt | tee difference.txt">
 <group name="system" />
 <input name="original_file">
  <file path="from.txt" />
 </input>
 <input name="modified_file">
  <file path="to.txt" />
 </input>
 <output name="difference_file">
  <fromfile path="difference.txt" />
 </output>
</program>

<program name="openjpeg_tif2j2k_simple"
  description="Encoding a RGB/Grayscale TIFF image to JPEG2000 (JP2)"
      command="image_to_j2k -i input.tif -o output.jp2 -SOP -EPH">
         <input name="inputfile" binary="true">
                <file path="input.tif" />
                <mime type="image/tif" />
         </input>
         <output name="outputimage" binary="true">
                <fromfile path="output.jp2" />
                <mime type="image/jp2" />
         </output>
</program>

<program name="openjpeg_tif2j2k"
 description="Encoding a RGB/Grayscale TIFF image to JPEG2000 (JP2)">
<command>
image_to_j2k -r %%compression%% -n %%resolutions%% -b %%codeblocksize%% -t %%tilesize%% -p %%progressionorder%% -s %%subsamplingfactor%% -i input.tif -o output.jp2 -SOP -EPH
</command>
   <input name="compression">
      <replace tag="compression"/>
   </input>
   <input name="resolutions">
      <replace tag="resolutions"/>
   </input>
   <input name="codeblocksize">
      <replace tag="codeblocksize"/>
   </input>
   <input name="tilesize">
      <replace tag="tilesize"/>
   </input>
   <input name="progressionorder">
     <replace tag="progressionorder"/>
   </input>
   <input name="subsamplingfactor">
     <replace tag="subsamplingfactor"/>
   </input>
   <input name="inputfile" binary="true">
         <file path="input.tif" />
      <mime type="image/tif" />
   </input>
   <output name="outputimage" binary="true">
        <fromfile path="output.jp2" />
      <mime type="image/jp2" />
   </output>
</program>

<program name="editconf_box"
  description="Generation of dodecahedric bounding box."
      timeout="1800" preparing_timeout="1200">
  <command>editconf -f protein_in.gro -o protein_out.gro -bt dodecahedron -d 1.2</command>
  <group name="GROMACS" />
  <input name="protein_in">
    <file path="protein_in.gro" />
  </input>
  <output name="protein_out">
    <fromfile path="protein_out.gro" />
  </output>
</program>

<program name="genbox_soluble"
  description="Fills box with water">
  <command>tar xzf topology_include.tgz ; 
genbox -cp protein_in.gro -cs spc216.gro -p protein.top -o protein_out.gro ; 
touch topology_include_files.itp ;
tar czf topology_include_files.tar.gz *.itp
</command>
  <group name="GROMACS" />
  <input name="GROMACS_protein_in_gro">
    <file path="protein_in.gro" />
  </input>
  <input name="GROMACS_topology_top">
    <file path="protein.top" />
  </input>
  <input name="GROMACS_topology_include_files_itp_tgz" binary="true">
    <file path="topology_include.tgz" />
  </input>
  <output name="GROMACS_topology_top">
    <fromfile path="protein.top" />
  </output>
  <output name="GROMACS_topology_include_files_itp_tgz" binary="true">
    <fromfile path="topology_include.tgz" />
  </output>
  <output name="GROMACS_protein_out_gro">
    <fromfile path="protein_out.gro" />
  </output>
</program>

<program name="genion_salt"
  description="Adding Na+ and Cl- ions to achieve neutrality">
<command>tar xzf topology_include.tgz ; 
echo SOL | genion -s protein-water.tpr -o protein-solvated.gro -conc 0.15 -neutral -p protein.top -pname NA -nname CL ;
touch topology_include_files.itp ;
tar czf topology_include_files.tar.gz *.itp
</command>
  <group name="GROMACS" />
  <input name="GROMACS_topology_top">
    <file path="protein.top" />
  </input>
  <input name="GROMACS_topology_include_files_itp_tgz" binary="true">
    <file path="topology_include.tgz" />
  </input>
  <input name="GROMACS_protein_in_tpr">
    <file path="protein-water.tpr" />
  </input>
  <output name="GROMACS_protein_out_gro">
    <fromfile path="protein-solvated.gro" />
  </output>
  <output name="GROMACS_topology_top">
    <fromfile path="protein.top" />
  </output>
  <output name="GROMACS_topology_include_files_itp_tgz" binary="true">
    <fromfile path="topology_include.tgz" />
  </output>
</program>