# HG changeset patch # User galaxyp # Date 1664373361 0 # Node ID 3c45645197f6258877f2650e18661c112d056101 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d diff -r 000000000000 -r 3c45645197f6 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Sep 28 13:56:01 2022 +0000 @@ -0,0 +1,1245 @@ + + 2.0.2 + 0 + + + 10.1101/gr.235028.118 + 10.1038/s41467-020-15456-w + + + http://pepquery.org/document.html + + +#import re +#import os.path +#def identifier_or_name($input1) + #if hasattr($input1, 'element_identifier') + #return $input1.element_identifier + #else + #return $input1.name + #end if +#end def +#def clean($name1) + #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fas|fasta|imzml|mzml|mzxml|mgf|raw)$','', $re.sub('.*/','', $name1.rstrip('.gz')))) + #return $name_clean +#end def +#def ln_name($ds) + #set $ext = '' + #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml') + #set $ext = ".mzML" + #else if $ds.is_of_type('mzxml') + #set $ext = ".mzXML" + #else if $ds.is_of_type('mgf') + #set $ext = ".mgf" + #else if $ds.is_of_type('thermo.raw') + #set $ext = ".raw" + #else if $ds.is_of_type('fasta') + #set $ext = ".fasta" + #end if + #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext) + #return $name +#end def + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 3c45645197f6 pepquery2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pepquery2.xml Wed Sep 28 13:56:01 2022 +0000 @@ -0,0 +1,931 @@ + + Peptide-centric search engine for novel peptide identification and validation. + + macros.xml + + + pepquery + + + + + + (cat 1>&2) + ]]> + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + ^[AC-IK-NP-TV-Yac-ik-np-tv-y]+(,[AC-IK-NP-TV-Yac-ik-np-tv-y]+)*$ + + + + + + + + + + + + + + + + ^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$ + + + + + + + ^[acgtuAGCTU]{60}[acgtuAGCTU]*$ + + + + + + + + + + + + + + + + + + + + + + + Currently supported dowloads: gencode:human, swissprot:human, refseq:human + + + + ^(swissprot|refseq|gencode):(human)$ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ^(PXD|MSV|JPST).*$ + + + + + + + + +
+ + + Currently supported set names start with: MS1 or TMT + + + + + + + + + + + + + +
+ + default: 1: Carbamidomethylation of C [57.02146372057] + + + + default: 2: Oxidation of M [15.99491461956] + + + + + + +
+ +
+ + + + + + + + + + + +
+ +
+
+ + + + + + +
+ +
+ + + + + + + + + + + + + + A comma-sepated range of integers from -2 to 2, e.g. '-1,0,1,2' Default: 0 + ^((-2,)?-1,)?0(,1(,2)?)?$ + + + + + +
+
+ + + + + + + + + + + + + + + +
+ + + 'ms_index' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history' + + + 'parameter.txt' in outputs_selected + + + + 'psm.txt' in outputs_selected + + + + + + + + 'psm_rank.txt' in outputs_selected + + + + + + + + 'psm_rank.mgf' in outputs_selected + + + 'psm_type.txt' in outputs_selected + + + + + + + 'psm_annotation.txt' in outputs_selected + + + + + + + 'detail.txt' in outputs_selected + + + + + + + + 'ptm.txt' in outputs_selected + + + + + + + 'ptm_detail.txt' in outputs_selected + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +