changeset 8:ea0a1d50c83f draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"

--- 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 ${on_string}" name="@NAME@">
@@ -240,7 +240,7 @@
                    type="data" label="FASTA files"
                    help="Specify one or more FASTA databases."/>
             <param name="identifier_parse_rule" type="text"
-                   label="identifier parse rule" value="^&gt;.*\|(.*)\|.*$">
+                   label="identifier parse rule" value="&gt;([^\s]*)">
                 <sanitizer>
                     <valid initial="string.printable">
                         <remove value="&apos;"/>
@@ -248,7 +248,7 @@
                 </sanitizer>
             </param>
             <param name="description_parse_rule" type="text"
-                   label="description parse rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$"
+                   label="description parse rule" value="&gt;(.*)"
                    help="Modify parse rules if needed.">
                 <sanitizer>
                     <valid initial="string.printable">
@@ -636,6 +636,8 @@
         <test expect_num_outputs="2">
             <param name="ftype" value=".mzxml" />
             <param name="fasta_files" value="bsa.fasta" />
+            <param name="identifier_parse_rule" value="^&gt;.*\|(.*)\|.*$" />
+            <param name="description_parse_rule" value="^&gt;.*\|.*\|[^ ]+ (.*) 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>