annotate idpassemble.xml @ 7:0fde0095493f draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 0854597c46f50e99a292a48f7f5521db99d26b2b"
author galaxyp
date Fri, 26 Jun 2020 17:33:35 -0400
parents 39eaac8f3f42
children 4b418a632bb0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
1 <?xml version="1.0"?>
5
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
2 <tool id="idpassemble" name="idpAssemble" version="@VERSION@.0">
0
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
4 <macros>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
5 <import>macros.xml</import>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
6 </macros>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
7 <expand macro="requirements" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
8 <stdio>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
9 <exit_code range="1:" level="fatal" description="Job Failed" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
10 <regex match="^Error:.*$" source="both" level="fatal" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
11 </stdio>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
12 <command>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
13 <![CDATA[
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
14 #if len($input) < 2
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
15 cp '${input}' output &&
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
16 #end if
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
17
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
18 idpAssemble
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
19 -MaxFDRScore $MaxFDRScore
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
20 -MinDistinctPeptides $filter_at_gene_level_condition.MinDistinctPeptides
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
21 -MinSpectra $filter_at_gene_level_condition.MinSpectra
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
22 -MinAdditionalPeptides $filter_at_gene_level_condition.MinAdditionalPeptides
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
23 -MinSpectraPerDistinctMatch $MinSpectraPerDistinctMatch
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
24 -MinSpectraPerDistinctPeptide $MinSpectraPerDistinctPeptide
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
25 -MaxProteinGroupsPerPeptide $MaxProteinGroupsPerPeptide
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
26 #if $filter_at_gene_level_condition.FilterAtGeneLevel
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
27 -FilterAtGeneLevel 1
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
28 #end if
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
29 -SummarizeSources 1
3
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
30
5
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
31 #if $AssignSourceHierarchyCondition.HasAssignSourceHierarchy
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
32 -AssignSourceHierarchy '$AssignSourceHierarchyCondition.AssignSourceHierarchy'
3
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
33 #end if
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
34
5
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
35 #if $IsobaricSampleMappingCondition.HasIsobaricSampleMapping
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
36 -IsobaricSampleMapping '$IsobaricSampleMappingCondition.IsobaricSampleMapping'
3
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
37 #end if
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
38
0
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
39 #if len($input) > 1
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
40 -MergedOutputFilepath output
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
41 #for $i in $input
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
42 '${i.file_name}'
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
43 #end for
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
44 #else
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
45 output
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
46 #end if
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
47 ]]>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
48 </command>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
49 <inputs>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
50 <param name="input" type="data" format="idpdb" label="Input idpDB(s)" multiple="true"/>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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." />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
52 <conditional name="filter_at_gene_level_condition">
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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')"/>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
54 <when value="1">
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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." />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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." />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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." />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
58 </when>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
59 <when value="0">
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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." />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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." />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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." />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
63 </when>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
64 </conditional>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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." />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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." />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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." />
5
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
68
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
69 <conditional name="AssignSourceHierarchyCondition">
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
70 <param name="HasAssignSourceHierarchy" type="boolean" truevalue="1" falsevalue="0" label="Assign sources to a hierarchy?"/>
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
71 <when value="1">
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
72 <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." />
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
73 </when>
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
74 <when value="0">
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
75 </when>
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
76 </conditional>
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
77 <conditional name="IsobaricSampleMappingCondition">
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
78 <param name="HasIsobaricSampleMapping" type="boolean" truevalue="1" falsevalue="0" label="Assign sample names to reporter ions?"/>
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
79 <when value="1">
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
80 <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." />
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
81 </when>
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
82 <when value="0">
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
83 </when>
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
84 </conditional>
0
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
85 </inputs>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
86 <outputs>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
87 <data format="idpdb" name="output" from_work_dir="output" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
88 </outputs>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
89 <tests>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
90 <test>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
91 <param name="input" value="201208-378803-mm.idpDB" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
92 <param name="MaxFDRScore" value="0.05" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
93 <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
94 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
95 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
96 <param name="MinSpectraPerDistinctMatch" value="1" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
97 <param name="MinSpectraPerDistinctPeptide" value="1" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
98 <param name="MaxProteinGroupsPerPeptide" value="10" />
2
dd33125925d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 1e51bed3a1c10c67ef0404216608e9333db04c64
galaxyp
parents: 0
diff changeset
99 <output name="output" file="201208-378803-mm-filtered.idpDB" compare="sim_size" delta="500000" />
0
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
100 </test>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
101 <test>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
102 <param name="input" value="201208-378803-msgf.idpDB" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
103 <param name="MaxFDRScore" value="0.05" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
104 <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
105 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
106 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
107 <param name="MinSpectraPerDistinctMatch" value="1" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
108 <param name="MinSpectraPerDistinctPeptide" value="1" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
109 <param name="MaxProteinGroupsPerPeptide" value="10" />
2
dd33125925d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 1e51bed3a1c10c67ef0404216608e9333db04c64
galaxyp
parents: 0
diff changeset
110 <output name="output" file="201208-378803-msgf-filtered.idpDB" compare="sim_size" delta="500000" />
0
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
111 </test>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
112 <test>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
113 <param name="input" value="201208-378803-cm.idpDB" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
114 <param name="MaxFDRScore" value="0.05" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
115 <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
116 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
117 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
118 <param name="MinSpectraPerDistinctMatch" value="1" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
119 <param name="MinSpectraPerDistinctPeptide" value="1" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
120 <param name="MaxProteinGroupsPerPeptide" value="10" />
5
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
121 <param name="HasAssignSourceHierarchy" value="1" />
3
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
122 <param name="AssignSourceHierarchy" value="assembly.tsv" ftype="tabular" />
2
dd33125925d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 1e51bed3a1c10c67ef0404216608e9333db04c64
galaxyp
parents: 0
diff changeset
123 <output name="output" file="201208-378803-cm-filtered.idpDB" compare="sim_size" delta="500000" />
0
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
124 </test>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
125 <test>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
126 <param name="input" value="201208-378803-mm.idpDB,201208-378803-msgf.idpDB,201208-378803-cm.idpDB" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
127 <param name="MaxFDRScore" value="0.05" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
128 <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
129 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
130 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
131 <param name="MinSpectraPerDistinctMatch" value="1" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
132 <param name="MinSpectraPerDistinctPeptide" value="1" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
133 <param name="MaxProteinGroupsPerPeptide" value="10" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
134 <output name="output" file="201208-378803.idpDB" compare="sim_size" delta="500000" />
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
135 </test>
3
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
136 <test>
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
137 <param name="input" value="201208-378803-embeddedGenesAndQuantitation.idpDB" />
5
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
138 <param name="HasAssignSourceHierarchy" value="1" />
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
139 <param name="HasIsobaricSampleMapping" value="1" />
3
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
140 <param name="IsobaricSampleMapping" value="mapping.tsv" ftype="tabular" />
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
141 <param name="AssignSourceHierarchy" value="assembly.tsv" ftype="tabular" />
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
142 <output name="output" file="201208-378803-embeddedGenesAndQuantitationWithMapping.idpDB" compare="sim_size" delta="500000" />
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
143 </test>
0
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
144 </tests>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
145 <help>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
146 <![CDATA[
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
147 **What it does**
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
148
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
149 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.
3
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
150
5
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
151 ====
3
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
152
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
153 **AssignSourceHierarchy**
5
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
154
3
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
155 The assembly file is a tab-delimited file with two columns that organizes the sources (individual runs) into a hierarchy.
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
156 The first column is the name of a source group, the second column is the source path or name to assign to that group.
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
157 A forward slash in the group name adds another level to the hierarchy (just like a directory path).
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
158
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
159 *A simple example:*
5
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
160
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
161 ::
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
162
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
163 /repA repA1.idpDB
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
164 /repA repA2.idpDB
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
165 /repB repB1.idpDB
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
166 /repB repB2.idpDB
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
167
3
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
168
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
169 *A multi-level example:*
5
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
170
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
171 ::
3
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
172
5
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
173 /A/1 A1_f1
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
174 /A/1 A1_f2
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
175 /A/2 A2_f1
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
176 /A/2 A2_f2
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
177 /B/1 B1_f1
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
178 /B/1 B1_f2
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
179 /B/2 B2_f1
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
180 /B/2 B2_f2
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
181
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
182 ====
3
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
183
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
184 **IsobaricSampleMapping**
5
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
185
3
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
186 The mapping file is a tab-delimited file with two columns. The first column is the full path to a source group,
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
187 the second column is a comma-delimited list of sample names, in ascending order of reporter ion mass. The special
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
188 sample name *Reference*, if present, will be used to normalize the other channels. Samples named *Empty* will be
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
189 ignored.
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
190
5
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
191
3
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
192 *iTRAQ-4plex example:*
5
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
193
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
194 ::
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
195
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
196 /Case/Group1_A123_B456_C789 A123,B456,C789,Reference
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
197 /Case/Group2_D123_E456_F789 D123,E456,F789,Reference
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
198 /Ctrl/Group3_X123_Y456_Z789 Reference,X123,Y456,Z789
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
199 /Ctrl/Group4_U123_V456_None U123,Reference,V456,Empty
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
200
3
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
201
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
202 *TMT-10plex example:*
5
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
203
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
204 ::
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
205
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
206 /Group1_Cases1-4_Controls1-4 Case1,Case2,Case3,Case4,Reference,Control1,Control2,Control3,Control4,Reference
39eaac8f3f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents: 4
diff changeset
207 /Group2_Cases5-8_Controls5-8 Case5,Case6,Case7,Case8,Reference,Control5,Control6,Control7,Control8,Reference
3
d562ee284f8a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
galaxyp
parents: 2
diff changeset
208
0
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
209 ]]>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
210 </help>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
211 <citations>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
212 <citation type="doi">10.1021/pr900360j</citation>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
213 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
214 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
215 </citations>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff changeset
216 </tool>