| Previous changeset 7:d253b379322b (2020-06-01) Next changeset 9:37d669de2828 (2021-02-19) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" |
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modified:
maxquant.xml |
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| diff -r d253b379322b -r ea0a1d50c83f maxquant.xml --- a/maxquant.xml Mon Jun 01 11:51:25 2020 -0400 +++ b/maxquant.xml Wed Jun 03 15:32:53 2020 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy2"> +<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy3"> <macros> <xml name="output" token_format="tabular" token_label="default description" token_name="default"> <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@"> @@ -240,7 +240,7 @@ type="data" label="FASTA files" help="Specify one or more FASTA databases."/> <param name="identifier_parse_rule" type="text" - label="identifier parse rule" value="^>.*\|(.*)\|.*$"> + label="identifier parse rule" value=">([^\s]*)"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> @@ -248,7 +248,7 @@ </sanitizer> </param> <param name="description_parse_rule" type="text" - label="description parse rule" value="^>.*\|.*\|[^ ]+ (.*) OS.*$" + label="description parse rule" value=">(.*)" help="Modify parse rules if needed."> <sanitizer> <valid initial="string.printable"> @@ -636,6 +636,8 @@ <test expect_num_outputs="2"> <param name="ftype" value=".mzxml" /> <param name="fasta_files" value="bsa.fasta" /> + <param name="identifier_parse_rule" value="^>.*\|(.*)\|.*$" /> + <param name="description_parse_rule" value="^>.*\|.*\|[^ ]+ (.*) OS.*$" /> <param name="min_unique_pep" value="1" /> <param name="ibaq" value="True" /> <param name="ibaqLogFit" value="False" /> @@ -687,7 +689,25 @@ - Thermo raw, mzML, mzXMLfiles (in parameter group section) - The datatype of all files has to be either 'thermo.raw', 'mzML' or 'mzXML'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes) -- Fasta file: specify parse rules accordingly, default rules are compatible with uniprot +- Fasta file: specify parse rules according to your fasta file (header). Some examples for different fasta headers: + + :: + + identifier parse rule description parse rule + + Uniprot identifier >.*\|(.*)\| >.*\|.*\|[^ ]+ (.*) OS + + NCBI accession >(gi\|[0-9]*) + + IPI accession >IPI:([^\| .]*) + + Everything after '>' >(.*) + + Up to first space >([^ ]*) + + Up to first tab character >([^\t]*) + + - Optional files: - Tabular file with experimental design template: @@ -730,7 +750,7 @@ **Output files** -Different output file options are available, most of them are part of the MaxQuant txt directory. +Different output file options are available, most of them are part of the MaxQuant txt directory. ]]></help> <expand macro="citations"/> </tool> |