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added:
ProteinInteractions.xml |
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| diff -r 5935066604a7 -r 830112c59150 ProteinInteractions.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ProteinInteractions.xml Tue Mar 15 15:36:37 2016 -0400 |
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| @@ -0,0 +1,61 @@ +<tool id="SAINT_ProteinInteractions" name="SAINT Output to Protein Interaction File"> + <description></description> + <command interpreter="python">ProteinInteractions.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 type="float" name="saint_cutoff" label="Saint Score Cutoff" value="0.8"/> + <param type="float" name="CPDB_cutoff" label="Consensus Path Database Score Cutoff" value="0.8"/> + <param type="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|error" + source="stdout" + level="fatal" + description="Unknown error"/> + <regex match="Error|error" + source="stderr" + level="fatal" + description="Unknown error"/> + <regex match="Error: bad bait" + source="stdout" + level="fatal" + description="Error: bad bait"/> + </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> +**Protein Interactions** + +This program will read in a SAINT 'list.txt' file and the interactions from ConsensusPathDB ( http://consensuspathdb.org/ ) and return all the interactions that we saw in our experiment in a format suitable for cytoscape. This allows us to filter before getting protein-protein interactions (PPI's) so that it doesn't affect our SAINT score or include interactions that don't score well. + +INPUT + +SAINT Output: SAINTexpress output. + +SAINT Score Cutoff: Saint score cutoff for import (between 0 and 1). + +Consensus Path Database Score Cutoff: Confidence of PPI from CPDB to include (between 0 and 1). + * low: no filtering + * medium: >0.5 + * high: >0.7 + * very high: >0.9 + +Species: Human, Yeast, or Mouse. + + </help> +</tool> \ No newline at end of file |