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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
author galaxyp
date Thu, 15 Dec 2016 17:12:33 -0500
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-1:000000000000 0:0d089906f752
1 <?xml version="1.0"?>
2 <tool id="idpassemble" name="idpAssemble" version="@VERSION@.0">
3 <description>Merge IDPicker databases from single files into a merged database, and filters the result at PSM/spectrum/peptide/protein/gene levels.</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <stdio>
9 <exit_code range="1:" level="fatal" description="Job Failed" />
10 <regex match="^Error:.*$" source="both" level="fatal" />
11 </stdio>
12 <command>
13 <![CDATA[
14 #if len($input) < 2
15 cp '${input}' output &&
16 #end if
17
18 idpAssemble
19 -MaxFDRScore $MaxFDRScore
20 -MinDistinctPeptides $filter_at_gene_level_condition.MinDistinctPeptides
21 -MinSpectra $filter_at_gene_level_condition.MinSpectra
22 -MinAdditionalPeptides $filter_at_gene_level_condition.MinAdditionalPeptides
23 -MinSpectraPerDistinctMatch $MinSpectraPerDistinctMatch
24 -MinSpectraPerDistinctPeptide $MinSpectraPerDistinctPeptide
25 -MaxProteinGroupsPerPeptide $MaxProteinGroupsPerPeptide
26 #if $filter_at_gene_level_condition.FilterAtGeneLevel
27 -FilterAtGeneLevel 1
28 #end if
29 -SummarizeSources 1
30 #if len($input) > 1
31 -MergedOutputFilepath output
32 #for $i in $input
33 '${i.file_name}'
34 #end for
35 #else
36 output
37 #end if
38 ]]>
39 </command>
40 <inputs>
41 <param name="input" type="data" format="idpdb" label="Input idpDB(s)" multiple="true"/>
42 <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." />
43 <conditional name="filter_at_gene_level_condition">
44 <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')"/>
45 <when value="1">
46 <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." />
47 <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." />
48 <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." />
49 </when>
50 <when value="0">
51 <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." />
52 <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." />
53 <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." />
54 </when>
55 </conditional>
56 <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." />
57 <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." />
58 <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." />
59 </inputs>
60 <outputs>
61 <data format="idpdb" name="output" from_work_dir="output" />
62 </outputs>
63 <tests>
64 <test>
65 <param name="input" value="201208-378803-mm.idpDB" />
66 <param name="MaxFDRScore" value="0.05" />
67 <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
68 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
69 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
70 <param name="MinSpectraPerDistinctMatch" value="1" />
71 <param name="MinSpectraPerDistinctPeptide" value="1" />
72 <param name="MaxProteinGroupsPerPeptide" value="10" />
73 <output name="output" file="201208-378803-mm.idpDB" compare="sim_size" delta="500000" />
74 </test>
75 <test>
76 <param name="input" value="201208-378803-msgf.idpDB" />
77 <param name="MaxFDRScore" value="0.05" />
78 <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
79 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
80 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
81 <param name="MinSpectraPerDistinctMatch" value="1" />
82 <param name="MinSpectraPerDistinctPeptide" value="1" />
83 <param name="MaxProteinGroupsPerPeptide" value="10" />
84 <output name="output" file="201208-378803-msgf.idpDB" compare="sim_size" delta="500000" />
85 </test>
86 <test>
87 <param name="input" value="201208-378803-cm.idpDB" />
88 <param name="MaxFDRScore" value="0.05" />
89 <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
90 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
91 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
92 <param name="MinSpectraPerDistinctMatch" value="1" />
93 <param name="MinSpectraPerDistinctPeptide" value="1" />
94 <param name="MaxProteinGroupsPerPeptide" value="10" />
95 <output name="output" file="201208-378803-cm.idpDB" compare="sim_size" delta="500000" />
96 </test>
97 <test>
98 <param name="input" value="201208-378803-mm.idpDB,201208-378803-msgf.idpDB,201208-378803-cm.idpDB" />
99 <param name="MaxFDRScore" value="0.05" />
100 <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
101 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
102 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
103 <param name="MinSpectraPerDistinctMatch" value="1" />
104 <param name="MinSpectraPerDistinctPeptide" value="1" />
105 <param name="MaxProteinGroupsPerPeptide" value="10" />
106 <output name="output" file="201208-378803.idpDB" compare="sim_size" delta="500000" />
107 </test>
108 </tests>
109 <help>
110 <![CDATA[
111 **What it does**
112
113 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.
114 ]]>
115 </help>
116 <citations>
117 <citation type="doi">10.1021/pr900360j</citation>
118 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
119 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
120 </citations>
121 </tool>