--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/idpassemble.xml	Thu Dec 15 17:12:33 2016 -0500
@@ -0,0 +1,121 @@
+<?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>