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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db |
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modified:
idpassemble.xml macros.xml |
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| diff -r 123813b3eed3 -r 39eaac8f3f42 idpassemble.xml --- a/idpassemble.xml Fri Nov 03 14:31:39 2017 -0400 +++ b/idpassemble.xml Tue Nov 21 13:19:10 2017 -0500 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="idpassemble" name="idpAssemble" version="@VERSION@.1"> +<tool id="idpassemble" name="idpAssemble" version="@VERSION@.0"> <description>Merge IDPicker databases from single files into a merged database, and filters the result at PSM/spectrum/peptide/protein/gene levels.</description> <macros> <import>macros.xml</import> @@ -28,12 +28,12 @@ #end if -SummarizeSources 1 - #if $AssignSourceHierarchy - -AssignSourceHierarchy '$AssignSourceHierarchy' + #if $AssignSourceHierarchyCondition.HasAssignSourceHierarchy + -AssignSourceHierarchy '$AssignSourceHierarchyCondition.AssignSourceHierarchy' #end if - #if $IsobaricSampleMapping - -IsobaricSampleMapping '$IsobaricSampleMapping' + #if $IsobaricSampleMappingCondition.HasIsobaricSampleMapping + -IsobaricSampleMapping '$IsobaricSampleMappingCondition.IsobaricSampleMapping' #end if #if len($input) > 1 @@ -65,8 +65,23 @@ <param argument="-MinSpectraPerDistinctMatch" type="integer" label="Min Filtered Spectra per Distinct Match" min="1" value="1" help="Distinct matches with fewer than this number of spectra will be excluded from the filtered data set." /> <param argument="-MinSpectraPerDistinctPeptide" type="integer" label="Min Filtered Spectra per Distinct Peptide" min="1" value="1" help="Distinct peptides with fewer than this number of spectra will be excluded from the filtered data set." /> <param argument="-MaxProteinGroupsPerPeptide" type="integer" label="Max Protein Groups per Distinct Peptide" min="0" value="10" help="Peptides that map to more than this number of protein groups will be excluded from the filtered data set. Highly ambiguous peptides are not very useful for quantitation." /> - <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." /> - <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." /> + + <conditional name="AssignSourceHierarchyCondition"> + <param name="HasAssignSourceHierarchy" type="boolean" truevalue="1" falsevalue="0" label="Assign sources to a hierarchy?"/> + <when value="1"> + <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." /> + </when> + <when value="0"> + </when> + </conditional> + <conditional name="IsobaricSampleMappingCondition"> + <param name="HasIsobaricSampleMapping" type="boolean" truevalue="1" falsevalue="0" label="Assign sample names to reporter ions?"/> + <when value="1"> + <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." /> + </when> + <when value="0"> + </when> + </conditional> </inputs> <outputs> <data format="idpdb" name="output" from_work_dir="output" /> @@ -103,6 +118,7 @@ <param name="MinSpectraPerDistinctMatch" value="1" /> <param name="MinSpectraPerDistinctPeptide" value="1" /> <param name="MaxProteinGroupsPerPeptide" value="10" /> + <param name="HasAssignSourceHierarchy" value="1" /> <param name="AssignSourceHierarchy" value="assembly.tsv" ftype="tabular" /> <output name="output" file="201208-378803-cm-filtered.idpDB" compare="sim_size" delta="500000" /> </test> @@ -119,6 +135,8 @@ </test> <test> <param name="input" value="201208-378803-embeddedGenesAndQuantitation.idpDB" /> + <param name="HasAssignSourceHierarchy" value="1" /> + <param name="HasIsobaricSampleMapping" value="1" /> <param name="IsobaricSampleMapping" value="mapping.tsv" ftype="tabular" /> <param name="AssignSourceHierarchy" value="assembly.tsv" ftype="tabular" /> <output name="output" file="201208-378803-embeddedGenesAndQuantitationWithMapping.idpDB" compare="sim_size" delta="500000" /> @@ -130,52 +148,63 @@ 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. +==== **AssignSourceHierarchy** + The assembly file is a tab-delimited file with two columns that organizes the sources (individual runs) into a hierarchy. The first column is the name of a source group, the second column is the source path or name to assign to that group. A forward slash in the group name adds another level to the hierarchy (just like a directory path). *A simple example:* -====== =========== -/repA repA1.idpDB -/repA repA2.idpDB -/repB repB1.idpDB -/repB repB2.idpDB -====== =========== + +:: + +/repA repA1.idpDB +/repA repA2.idpDB +/repB repB1.idpDB +/repB repB2.idpDB + *A multi-level example:* -===== =========== -/A/1 A1_f1 -/A/1 A1_f2 -/A/2 A2_f1 -/A/2 A2_f2 -/B/1 B1_f1 -/B/1 B1_f2 -/B/2 B2_f1 -/B/2 B2_f2 -===== =========== + +:: +/A/1 A1_f1 +/A/1 A1_f2 +/A/2 A2_f1 +/A/2 A2_f2 +/B/1 B1_f1 +/B/1 B1_f2 +/B/2 B2_f1 +/B/2 B2_f2 + +==== **IsobaricSampleMapping** + The mapping file is a tab-delimited file with two columns. The first column is the full path to a source group, the second column is a comma-delimited list of sample names, in ascending order of reporter ion mass. The special sample name *Reference*, if present, will be used to normalize the other channels. Samples named *Empty* will be ignored. + *iTRAQ-4plex example:* -=============================== ========================== -/Case/Group1_A123_B456_C789 A123,B456,C789,Reference -/Case/Group2_D123_E456_F789 D123,E456,F789,Reference -/Control/Group3_X123_Y456_Z789 Reference,X123,Y456,Z789 -/Control/Group4_U123_V456 U123,Reference,V456,Empty -=============================== ========================== + +:: + +/Case/Group1_A123_B456_C789 A123,B456,C789,Reference +/Case/Group2_D123_E456_F789 D123,E456,F789,Reference +/Ctrl/Group3_X123_Y456_Z789 Reference,X123,Y456,Z789 +/Ctrl/Group4_U123_V456_None U123,Reference,V456,Empty + *TMT-10plex example:* -============================= ================================================================================ -/Group1_Cases1-4_Controls1-4 Case1,Case2,Case3,Case4,Reference,Control1,Control2,Control3,Control4,Reference -/Group2_Cases5-8_Controls5-8 Case5,Case6,Case7,Case8,Reference,Control5,Control6,Control7,Control8,Reference -============================= ================================================================================ + +:: + +/Group1_Cases1-4_Controls1-4 Case1,Case2,Case3,Case4,Reference,Control1,Control2,Control3,Control4,Reference +/Group2_Cases5-8_Controls5-8 Case5,Case6,Case7,Case8,Reference,Control5,Control6,Control7,Control8,Reference ]]> </help> |
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| diff -r 123813b3eed3 -r 39eaac8f3f42 macros.xml --- a/macros.xml Fri Nov 03 14:31:39 2017 -0400 +++ b/macros.xml Tue Nov 21 13:19:10 2017 -0500 |
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| @@ -1,8 +1,8 @@ <macros> - <token name="@VERSION@">3.0.11392</token> + <token name="@VERSION@">3.0.11579</token> <xml name="requirements"> <requirements> - <requirement type="package" version="3_0_11392">bumbershoot</requirement> + <requirement type="package" version="3_0_11579">bumbershoot</requirement> <yield/> </requirements> </xml> |