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added:
ProteinInteractions_v2.xml |
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| diff -r cd2c68e1b1ae -r fd6f8df5a043 ProteinInteractions_v2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ProteinInteractions_v2.xml Thu Nov 19 11:17:15 2015 -0500 |
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| @@ -0,0 +1,36 @@ +<tool id="SAINT_ProteinInteractions_v2" name="SAINT Output to Protein Interaction File"> + <description></description> + <command interpreter="python">ProteinInteractions_v2.py $input $saint_cutoff $CPDB_cutoff $species $Cytoscape_File \$INSTALL_RUN_PATH/</command> + <requirements> + <requirement type="set_environment">INSTALL_RUN_PATH</requirement> + </requirements> + <inputs> + <param format="txt" name="input" type="data" label="SAINT Output"/> + <param format="float" name="saint_cutoff" label="Saint Score Cutoff"/> + <param format="float" name="CPDB_cutoff" label="Consensus Path Database Score Cutoff"/> + <param format="select" name="species" label="Species"> + <option value="Human">Human</option> + <option value="Yeast">Yeast</option> + <option value="Mouse">Mouse</option> + </param> + </inputs> + <outputs> + <data format="sif" name="Cytoscape_File" label="Cytoscape File"/> + </outputs> + <stdio> + <regex match="error" + source="stdout" + level="fatal" + description="Unknown error"/> + </stdio> + + <tests> + <test> + <param name="input" value="fa_gc_content_input.fa"/> + <output name="out_file1" file="fa_gc_content_output.txt"/> + </test> + </tests> + <help> + This program will read in a SAINT 'list.txt' file and the interactions from the consensus path db database and return all the interactions that we saw in our experiment in a format suitable for cytoscape. This allows us to filter before getting PPIs so that it doesn't affect our SAINT score or include interactions that don't score well + </help> +</tool> \ No newline at end of file |