| Previous changeset 2:ef46866326ef (2024-07-16) Next changeset 4:e969a182e3cb (2024-12-13) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit b1b03bb7cd31c1ec806b286d6c9444428b358e15 |
|
modified:
fragpipe.xml macros.xml |
| b |
| diff -r ef46866326ef -r da9ebef968bd fragpipe.xml --- a/fragpipe.xml Tue Jul 16 06:55:53 2024 +0000 +++ b/fragpipe.xml Thu Sep 12 08:06:44 2024 +0000 |
| b |
| @@ -154,6 +154,7 @@ <param name="database_name" value="default/test.fasta" ftype="fasta"/> <param name="manifest" value="default/test.manifest" ftype="tabular"/> <param name="workflow_name" value="Default"/> + <param name="label_free_quantification_run" value="ionquant"/> <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/> <param name="license_agreements" value="true"/> <output name="concat_psm_tsv" ftype="tabular"> |
| b |
| diff -r ef46866326ef -r da9ebef968bd macros.xml --- a/macros.xml Tue Jul 16 06:55:53 2024 +0000 +++ b/macros.xml Thu Sep 12 08:06:44 2024 +0000 |
| [ |
| @@ -1,7 +1,7 @@ <macros> <import>msfragger_macros.xml</import> <token name="@TOOL_VERSION@">20.0</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement> @@ -719,7 +719,7 @@ <when value="no"/> <when value="ionquant"> <section name="ionquant" expanded="false" title="IonQuant Label-Free Quantification"> - <param name="mbr" type="select" optional="true" label="Match between runs (MBR)" help="ionquant.mbr"> + <param name="mbr_select" type="select" optional="true" label="Match between runs (MBR)" help="ionquant.mbr"> <option value="0">No</option> <option value="1">Yes</option> </param> @@ -821,11 +821,8 @@ #set $wfdict['ionquant.run-ionquant'] = 'true' #set $wfdict['freequant.run-freequant'] = 'false' #set $cxt = $prfx.ionquant - #if $cxt.mbr != 'None' - #set $wfdict['ionquant.mbr'] = $cxt.mbr - #end if - #if $cxt.maxlfqbr is not None - #set $wfdict['ionquant.maxlfqbr'] = $cxt.maxlfqbr + #if $cxt.mbr_select != 'None' + #set $wfdict['ionquant.mbr'] = $cxt.mbr_select #end if #if $cxt.normalization != 'None' #set $wfdict['ionquant.normalization'] = $cxt.normalization |