Mercurial > repos > galaxyp > idpassemble
changeset 3:d562ee284f8a draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
| author | galaxyp |
|---|---|
| date | Thu, 02 Nov 2017 14:15:13 -0400 |
| parents | dd33125925d9 |
| children | 123813b3eed3 |
| files | idpassemble.xml test-data/201208-378803-embeddedGenesAndQuantitationWithMapping.idpDB test-data/201208-378803.idpDB test-data/assembly.tsv test-data/mapping.tsv |
| diffstat | 5 files changed, 68 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- a/idpassemble.xml Fri Oct 06 15:00:48 2017 -0400 +++ b/idpassemble.xml Thu Nov 02 14:15:13 2017 -0400 @@ -27,6 +27,15 @@ -FilterAtGeneLevel 1 #end if -SummarizeSources 1 + + #if $AssignSourceHierarchy + -AssignSourceHierarchy '$AssignSourceHierarchy' + #end if + + #if $IsobaricSampleMapping + -IsobaricSampleMapping '$IsobaricSampleMapping' + #end if + #if len($input) > 1 -MergedOutputFilepath output #for $i in $input @@ -56,6 +65,8 @@ <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." /> </inputs> <outputs> <data format="idpdb" name="output" from_work_dir="output" /> @@ -92,6 +103,7 @@ <param name="MinSpectraPerDistinctMatch" value="1" /> <param name="MinSpectraPerDistinctPeptide" value="1" /> <param name="MaxProteinGroupsPerPeptide" value="10" /> + <param name="AssignSourceHierarchy" value="assembly.tsv" ftype="tabular" /> <output name="output" file="201208-378803-cm-filtered.idpDB" compare="sim_size" delta="500000" /> </test> <test> @@ -105,12 +117,66 @@ <param name="MaxProteinGroupsPerPeptide" value="10" /> <output name="output" file="201208-378803.idpDB" compare="sim_size" delta="500000" /> </test> + <test> + <param name="input" value="201208-378803-embeddedGenesAndQuantitation.idpDB" /> + <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" /> + </test> </tests> <help> <![CDATA[ **What it does** Merges and filters one or more IDPicker 3 idpDB files into a combined idpDB file. Protein assembly (e.g. parsimony) is conducted on the combined set of proteins. + + +**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 +====== =========== + +*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 +===== =========== + + +**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 +=============================== ========================== + +*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 +============================= ================================================================================ + ]]> </help> <citations>