Mercurial > repos > galaxyp > idpassemble

annotate idpassemble.xml @ 14:87f2a3c9425b 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 commit 91950fbabd1db1b35e77bfa26c0d2ffc941ffceb
author galaxyp
date Fri, 03 Nov 2017 14:35:57 -0400
parents bc374b8b9d76
children 4aa6a8331445
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
1 <?xml version="1.0"?>
13
bc374b8b9d76 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents: 12
diff changeset
2 <tool id="idpassemble" name="idpAssemble" version="@VERSION@.1">
8
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
3 <description>Merge IDPicker databases from single files into a merged database, and filters the result at PSM/spectrum/peptide/protein/gene levels.</description>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
4 <macros>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
5 <import>macros.xml</import>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
6 </macros>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
7 <expand macro="requirements" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
8 <stdio>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
9 <exit_code range="1:" level="fatal" description="Job Failed" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
10 <regex match="^Error:.*$" source="both" level="fatal" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
11 </stdio>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
12 <command>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
13 <![CDATA[
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
14 #if len($input) < 2
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
15 cp '${input}' output &&
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
16 #end if
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
17
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
18 idpAssemble
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
19 -MaxFDRScore $MaxFDRScore
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
20 -MinDistinctPeptides $filter_at_gene_level_condition.MinDistinctPeptides
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
21 -MinSpectra $filter_at_gene_level_condition.MinSpectra
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
22 -MinAdditionalPeptides $filter_at_gene_level_condition.MinAdditionalPeptides
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
23 -MinSpectraPerDistinctMatch $MinSpectraPerDistinctMatch
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
24 -MinSpectraPerDistinctPeptide $MinSpectraPerDistinctPeptide
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
25 -MaxProteinGroupsPerPeptide $MaxProteinGroupsPerPeptide
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
26 #if $filter_at_gene_level_condition.FilterAtGeneLevel
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
27 -FilterAtGeneLevel 1
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
28 #end if
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
29 -SummarizeSources 1
10
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
30
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
31 #if $AssignSourceHierarchy
14
87f2a3c9425b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 91950fbabd1db1b35e77bfa26c0d2ffc941ffceb
galaxyp
parents: 13
diff changeset
32 -AssignSourceHierarchy '$AssignSourceHierarchy'
10
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
33 #end if
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
34
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
35 #if $IsobaricSampleMapping
14
87f2a3c9425b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 91950fbabd1db1b35e77bfa26c0d2ffc941ffceb
galaxyp
parents: 13
diff changeset
36 -IsobaricSampleMapping '$IsobaricSampleMapping'
10
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
37 #end if
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
38
8
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
39 #if len($input) > 1
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
40 -MergedOutputFilepath output
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
41 #for $i in $input
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
42 '${i.file_name}'
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
43 #end for
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
44 #else
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
45 output
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
46 #end if
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
47 ]]>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
48 </command>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
49 <inputs>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
50 <param name="input" type="data" format="idpdb" label="Input idpDB(s)" multiple="true"/>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
51 <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." />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
52 <conditional name="filter_at_gene_level_condition">
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
53 <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')"/>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
54 <when value="1">
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
55 <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." />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
56 <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." />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
57 <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." />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
58 </when>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
59 <when value="0">
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
60 <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." />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
61 <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." />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
62 <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." />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
63 </when>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
64 </conditional>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
65 <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." />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
66 <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." />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
67 <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." />
10
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
68 <param argument="-AssignSourceHierarchy" type="data" format="tabular" optional="true" label="Assign source files to groups" help="A tab-delimited file that organizes source files (e.g. individual runs in a fractionated experiment) into groups. See below for more details." />
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
69 <param argument="-IsobaricSampleMapping" type="data" format="tabular" optional="true" label="Assign sample names to reporter ions" help="A tab-delimited file that gives sample names to isobaric reporter ion channels (i.e. iTRAQ, TMT) across a given source group. See below for more details." />
8
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
70 </inputs>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
71 <outputs>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
72 <data format="idpdb" name="output" from_work_dir="output" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
73 </outputs>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
74 <tests>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
75 <test>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
76 <param name="input" value="201208-378803-mm.idpDB" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
77 <param name="MaxFDRScore" value="0.05" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
78 <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
79 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
80 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
81 <param name="MinSpectraPerDistinctMatch" value="1" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
82 <param name="MinSpectraPerDistinctPeptide" value="1" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
83 <param name="MaxProteinGroupsPerPeptide" value="10" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
84 <output name="output" file="201208-378803-mm-filtered.idpDB" compare="sim_size" delta="500000" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
85 </test>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
86 <test>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
87 <param name="input" value="201208-378803-msgf.idpDB" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
88 <param name="MaxFDRScore" value="0.05" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
89 <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
90 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
91 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
92 <param name="MinSpectraPerDistinctMatch" value="1" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
93 <param name="MinSpectraPerDistinctPeptide" value="1" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
94 <param name="MaxProteinGroupsPerPeptide" value="10" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
95 <output name="output" file="201208-378803-msgf-filtered.idpDB" compare="sim_size" delta="500000" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
96 </test>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
97 <test>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
98 <param name="input" value="201208-378803-cm.idpDB" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
99 <param name="MaxFDRScore" value="0.05" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
100 <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
101 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
102 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
103 <param name="MinSpectraPerDistinctMatch" value="1" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
104 <param name="MinSpectraPerDistinctPeptide" value="1" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
105 <param name="MaxProteinGroupsPerPeptide" value="10" />
10
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
106 <param name="AssignSourceHierarchy" value="assembly.tsv" ftype="tabular" />
8
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
107 <output name="output" file="201208-378803-cm-filtered.idpDB" compare="sim_size" delta="500000" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
108 </test>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
109 <test>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
110 <param name="input" value="201208-378803-mm.idpDB,201208-378803-msgf.idpDB,201208-378803-cm.idpDB" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
111 <param name="MaxFDRScore" value="0.05" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
112 <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
113 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
114 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
115 <param name="MinSpectraPerDistinctMatch" value="1" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
116 <param name="MinSpectraPerDistinctPeptide" value="1" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
117 <param name="MaxProteinGroupsPerPeptide" value="10" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
118 <output name="output" file="201208-378803.idpDB" compare="sim_size" delta="500000" />
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
119 </test>
10
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
120 <test>
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
121 <param name="input" value="201208-378803-embeddedGenesAndQuantitation.idpDB" />
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
122 <param name="IsobaricSampleMapping" value="mapping.tsv" ftype="tabular" />
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
123 <param name="AssignSourceHierarchy" value="assembly.tsv" ftype="tabular" />
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
124 <output name="output" file="201208-378803-embeddedGenesAndQuantitationWithMapping.idpDB" compare="sim_size" delta="500000" />
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
125 </test>
8
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
126 </tests>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
127 <help>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
128 <![CDATA[
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
129 **What it does**
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
130
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
131 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.
10
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
132
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
133
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
134 **AssignSourceHierarchy**
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
135 The assembly file is a tab-delimited file with two columns that organizes the sources (individual runs) into a hierarchy.
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
136 The first column is the name of a source group, the second column is the source path or name to assign to that group.
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
137 A forward slash in the group name adds another level to the hierarchy (just like a directory path).
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
138
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
139 *A simple example:*
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
140 ====== ===========
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
141 /repA repA1.idpDB
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
142 /repA repA2.idpDB
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
143 /repB repB1.idpDB
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
144 /repB repB2.idpDB
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
145 ====== ===========
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
146
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
147 *A multi-level example:*
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
148 ===== ===========
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
149 /A/1 A1_f1
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
150 /A/1 A1_f2
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
151 /A/2 A2_f1
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
152 /A/2 A2_f2
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
153 /B/1 B1_f1
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
154 /B/1 B1_f2
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
155 /B/2 B2_f1
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
156 /B/2 B2_f2
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
157 ===== ===========
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
158
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
159
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
160 **IsobaricSampleMapping**
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
161 The mapping file is a tab-delimited file with two columns. The first column is the full path to a source group,
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
162 the second column is a comma-delimited list of sample names, in ascending order of reporter ion mass. The special
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
163 sample name *Reference*, if present, will be used to normalize the other channels. Samples named *Empty* will be
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
164 ignored.
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
165
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
166 *iTRAQ-4plex example:*
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
167 =============================== ==========================
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
168 /Case/Group1_A123_B456_C789 A123,B456,C789,Reference
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
169 /Case/Group2_D123_E456_F789 D123,E456,F789,Reference
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
170 /Control/Group3_X123_Y456_Z789 Reference,X123,Y456,Z789
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
171 /Control/Group4_U123_V456 U123,Reference,V456,Empty
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
172 =============================== ==========================
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
173
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
174 *TMT-10plex example:*
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
175 ============================= ================================================================================
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
176 /Group1_Cases1-4_Controls1-4 Case1,Case2,Case3,Case4,Reference,Control1,Control2,Control3,Control4,Reference
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
177 /Group2_Cases5-8_Controls5-8 Case5,Case6,Case7,Case8,Reference,Control5,Control6,Control7,Control8,Reference
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
178 ============================= ================================================================================
1196c09b6d4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 8
diff changeset
179
8
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
180 ]]>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
181 </help>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
182 <citations>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
183 <citation type="doi">10.1021/pr900360j</citation>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
184 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
185 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
186 </citations>
e0ff9e45c273 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot
galaxyp
parents:
diff changeset
187 </tool>