Mercurial > repos > galaxyp > idpassemble

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING	Thu Dec 15 17:12:33 2016 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Thu Dec 15 17:12:33 2016 -0500
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+GalaxyP - idpAssemble
+====================
+
+* Home: <https://github.com/galaxyproteomics/tools-galaxyp/>
+* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/idpassemble>
+* Tool ID: `idpassemble`
+
+
+Description
+-----------
+
+Bumbershoot idpAssemble, a part of Bumbershoot IDPicker.
+
+See:
+
+* <http://fenchurch.mc.vanderbilt.edu/>
+
+
+GalaxyP Community
+-----------------
+
+Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at:
+
+<https://github.com/galaxyproteomics>
+
+
+License
+-------
+
+Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below.
+
+To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty.
+
+You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>.
+
+You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.
+
+
+Contributing
+------------
+
+Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://github.com/galaxyproteomics/tools-galaxyp/>
+
+
+Authors
+-------
+
+Authors and contributors:
+
+* Matt Chambers <matt.chambers42@gmail.com>
+  Vanderbilt University Medical Center
+
+* John Chilton <jmchilton@gmail.com>
+  Minnesota Supercomputing Institute, University of Minnesota
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/idpassemble.xml	Thu Dec 15 17:12:33 2016 -0500
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+<?xml version="1.0"?>
+<tool id="idpassemble" name="idpAssemble" version="@VERSION@.0">
+    <description>Merge IDPicker databases from single files into a merged database, and filters the result at PSM/spectrum/peptide/protein/gene levels.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Job Failed" />
+        <regex match="^Error:.*$" source="both" level="fatal" />
+    </stdio>
+    <command>
+<![CDATA[
+        #if len($input) < 2
+        cp '${input}' output &&
+        #end if
+
+        idpAssemble
+            -MaxFDRScore $MaxFDRScore
+            -MinDistinctPeptides $filter_at_gene_level_condition.MinDistinctPeptides
+            -MinSpectra $filter_at_gene_level_condition.MinSpectra
+            -MinAdditionalPeptides $filter_at_gene_level_condition.MinAdditionalPeptides
+            -MinSpectraPerDistinctMatch $MinSpectraPerDistinctMatch
+            -MinSpectraPerDistinctPeptide $MinSpectraPerDistinctPeptide
+            -MaxProteinGroupsPerPeptide $MaxProteinGroupsPerPeptide
+            #if $filter_at_gene_level_condition.FilterAtGeneLevel
+            -FilterAtGeneLevel 1
+            #end if
+            -SummarizeSources 1
+            #if len($input) > 1
+                -MergedOutputFilepath output
+                #for $i in $input
+                    '${i.file_name}'
+                #end for
+            #else
+                output
+            #end if
+]]>
+    </command>
+    <inputs>
+        <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" 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" 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" 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" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="201208-378803-mm.idpDB" />
+            <param name="MaxFDRScore" value="0.05" />
+            <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
+            <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
+            <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
+            <param name="MinSpectraPerDistinctMatch" value="1" />
+            <param name="MinSpectraPerDistinctPeptide" value="1" />
+            <param name="MaxProteinGroupsPerPeptide" value="10" />
+            <output name="output" file="201208-378803-mm.idpDB" compare="sim_size" delta="500000" />
+        </test>
+        <test>
+            <param name="input" value="201208-378803-msgf.idpDB" />
+            <param name="MaxFDRScore" value="0.05" />
+            <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
+            <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
+            <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
+            <param name="MinSpectraPerDistinctMatch" value="1" />
+            <param name="MinSpectraPerDistinctPeptide" value="1" />
+            <param name="MaxProteinGroupsPerPeptide" value="10" />
+            <output name="output" file="201208-378803-msgf.idpDB" compare="sim_size" delta="500000" />
+        </test>
+        <test>
+            <param name="input" value="201208-378803-cm.idpDB" />
+            <param name="MaxFDRScore" value="0.05" />
+            <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
+            <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
+            <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
+            <param name="MinSpectraPerDistinctMatch" value="1" />
+            <param name="MinSpectraPerDistinctPeptide" value="1" />
+            <param name="MaxProteinGroupsPerPeptide" value="10" />
+            <output name="output" file="201208-378803-cm.idpDB" compare="sim_size" delta="500000" />
+        </test>
+        <test>
+            <param name="input" value="201208-378803-mm.idpDB,201208-378803-msgf.idpDB,201208-378803-cm.idpDB" />
+            <param name="MaxFDRScore" value="0.05" />
+            <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
+            <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
+            <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
+            <param name="MinSpectraPerDistinctMatch" value="1" />
+            <param name="MinSpectraPerDistinctPeptide" value="1" />
+            <param name="MaxProteinGroupsPerPeptide" value="10" />
+            <output name="output" file="201208-378803.idpDB" compare="sim_size" delta="500000" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Merges and filters one or more IDPicker 3 idpDB files into a combined idpDB file. Protein assembly (e.g. parsimony) is conducted on the combined set of proteins.
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1021/pr900360j</citation>
+        <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
+          year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Dec 15 17:12:33 2016 -0500
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+<macros>
+    <token name="@VERSION@">3.0.10246</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="3_0_10246">bumbershoot</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+</macros>
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