Mercurial > repos > galaxyp > idpassemble

changeset 2:98f4f743b38f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit d571b106668cb1e749d6235abf5d2b6224c47d74
author galaxyp
date Mon, 12 Dec 2016 16:56:56 -0500
parents 92d81b01bc76
children e34b0740d53d
files COPYING README.md idpassemble.xml test-data/201208-378803-cm.idpDB test-data/201208-378803-mm.idpDB test-data/201208-378803-msgf.idpDB test-data/201208-378803.idpDB test-data/input/201208-378803-cm.idpDB test-data/input/201208-378803-mm.idpDB test-data/input/201208-378803-msgf.idpDB tool_dependencies.xml
diffstat 2 files changed, 12 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/idpassemble.xml	Tue Sep 15 17:50:02 2015 -0400
+++ b/idpassemble.xml	Mon Dec 12 16:56:56 2016 -0500
@@ -2,7 +2,7 @@
 <tool id="idpassemble" name="idpAssemble" version="0.1.0">
     <description>Merge IDPicker databases from single files into a merged database, and filters the result at PSM/spectrum/peptide/protein/gene levels.</description>
     <requirements>
-        <requirement type="package" version="3.0.8789">bumbershoot</requirement>
+        <requirement type="package" version="3.0.10185">bumbershoot</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Job Failed" />
@@ -37,24 +37,24 @@
 ]]>
     </command>
     <inputs>
-        <param name="input" type="data" format="idpdb" label="Input File(s)" multiple="true"/>
-        <param argument="-MaxFDRScore" type="float" label="Max FDR Score" value="0.05" help="Peptide-spectrum-matches (PSMs) with an FDR score (interpolated Q-value) higher than this will be excluded from the filtered data set." />
+        <param name="input" type="data" format="idpdb" label="Input idpDB(s)" multiple="true"/>
+        <param argument="-MaxFDRScore" type="float" label="Max FDR Score" min="0.00000001" value="0.05" help="Peptide-spectrum-matches (PSMs) with an FDR score (interpolated Q-value) higher than this will be excluded from the filtered data set." />
         <conditional name="filter_at_gene_level_condition">
             <param argument="-FilterAtGeneLevel" type="boolean" truevalue="1" falsevalue="0" label="Filter at Gene Level" help="Apply filters at the gene level (i.e. 'min distinct peptides per gene group' instead of 'min distinct peptides per protein group')"/>
             <when value="1">
-                <param argument="-MinDistinctPeptides" type="integer" label="Min Distinct Peptides per Gene Group" value="2" help="Gene groups with fewer than this number of peptides will be excluded from the filtered data set." />
-                <param argument="-MinSpectra" type="integer" label="Min Filtered Spectra per Gene Group" value="2" help="Gene groups with fewer than this number of spectra will be excluded from the filtered data set." />
-                <param argument="-MinAdditionalPeptides" type="integer" label="Min Additional Peptides per Gene Group" value="1" help="Gene groups that are not necessary to explain the presence of at least this many extra peptides will be from the filtered data set. A value of 1 means that each gene group must explain at least 1 peptide that other gene groups do not explain." />
+                <param argument="-MinDistinctPeptides" type="integer" label="Min Distinct Peptides per Gene Group" min="1" value="2" help="Gene groups with fewer than this number of peptides will be excluded from the filtered data set." />
+                <param argument="-MinSpectra" type="integer" label="Min Filtered Spectra per Gene Group" min="1" value="2" help="Gene groups with fewer than this number of spectra will be excluded from the filtered data set." />
+                <param argument="-MinAdditionalPeptides" type="integer" label="Min Additional Peptides per Gene Group" min="0" value="1" help="Gene groups that are not necessary to explain the presence of at least this many extra peptides will be from the filtered data set. A value of 1 means that each gene group must explain at least 1 peptide that other gene groups do not explain." />
             </when>
             <when value="0">
-                <param argument="-MinDistinctPeptides" type="integer" label="Min Distinct Peptides per Protein Group" value="2" help="Protein groups with fewer than this number of peptides will be excluded from the filtered data set." />
-                <param argument="-MinSpectra" type="integer" label="Min Filtered Spectra per Protein Group" value="2" help="Protein groups with fewer than this number of spectra will be excluded from the filtered data set." />
-                <param argument="-MinAdditionalPeptides" type="integer" label="Min Additional Peptides per Protein Group" value="1" help="Protein groups that are not necessary to explain the presence of at least this many extra peptides will be from the filtered data set. A value of 1 means that each protein group must explain at least 1 peptide that other protein groups do not explain." />
+                <param argument="-MinDistinctPeptides" type="integer" label="Min Distinct Peptides per Protein Group" min="1" value="2" help="Protein groups with fewer than this number of peptides will be excluded from the filtered data set." />
+                <param argument="-MinSpectra" type="integer" label="Min Filtered Spectra per Protein Group" min="1" value="2" help="Protein groups with fewer than this number of spectra will be excluded from the filtered data set." />
+                <param argument="-MinAdditionalPeptides" type="integer" label="Min Additional Peptides per Protein Group" min="0" value="1" help="Protein groups that are not necessary to explain the presence of at least this many extra peptides will be from the filtered data set. A value of 1 means that each protein group must explain at least 1 peptide that other protein groups do not explain." />
             </when>
         </conditional>
-        <param argument="-MinSpectraPerDistinctMatch" type="integer" label="Min Filtered Spectra per Distinct Match" value="1" help="Distinct matches with fewer than this number of spectra will be excluded from the filtered data set." />
-        <param argument="-MinSpectraPerDistinctPeptide" type="integer" label="Min Filtered Spectra per Distinct Peptide" value="1" help="Distinct peptides with fewer than this number of spectra will be excluded from the filtered data set." />
-        <param argument="-MaxProteinGroupsPerPeptide" type="integer" label="Max Protein Groups per Distinct Peptide" value="10" help="Peptides that map to more than this number of protein groups will be excluded from the filtered data set. Highly ambiguous peptides are not very useful for quantitation." />
+        <param argument="-MinSpectraPerDistinctMatch" type="integer" label="Min Filtered Spectra per Distinct Match" min="1" value="1" help="Distinct matches with fewer than this number of spectra will be excluded from the filtered data set." />
+        <param argument="-MinSpectraPerDistinctPeptide" type="integer" label="Min Filtered Spectra per Distinct Peptide" min="1" value="1" help="Distinct peptides with fewer than this number of spectra will be excluded from the filtered data set." />
+        <param argument="-MaxProteinGroupsPerPeptide" type="integer" label="Max Protein Groups per Distinct Peptide" min="0" value="10" help="Peptides that map to more than this number of protein groups will be excluded from the filtered data set. Highly ambiguous peptides are not very useful for quantitation." />
     </inputs>
     <outputs>
         <data format="idpdb" name="output" from_work_dir="output" />
--- a/tool_dependencies.xml	Tue Sep 15 17:50:02 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="bumbershoot" version="3.0.8789">
-    <repository changeset_revision="d9c7584f69f6" name="package_bumbershoot_3_0_8789" owner="galaxyp" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-  </package>
-</tool_dependency>