# 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 $name
+#end def
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diff -r 000000000000 -r 3c45645197f6 pepquery2.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pepquery2.xml Wed Sep 28 13:56:01 2022 +0000
@@ -0,0 +1,931 @@
+
+ Peptide-centric search engine for novel peptide identification and validation.
+
+ macros.xml
+
+
+ pepquery
+
+
+
+
+
+ (cat 1>&2)
+ ]]>
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+ ^[AC-IK-NP-TV-Yac-ik-np-tv-y]+(,[AC-IK-NP-TV-Yac-ik-np-tv-y]+)*$
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+ ^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$
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+ ^[acgtuAGCTU]{60}[acgtuAGCTU]*$
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+ Currently supported dowloads: gencode:human, swissprot:human, refseq:human
+
+
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+ ^(swissprot|refseq|gencode):(human)$
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+ ^(PXD|MSV|JPST).*$
+
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+ Currently supported set names start with: MS1 or TMT
+
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+ default: 1: Carbamidomethylation of C [57.02146372057]
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+ default: 2: Oxidation of M [15.99491461956]
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+ A comma-sepated range of integers from -2 to 2, e.g. '-1,0,1,2' Default: 0
+ ^((-2,)?-1,)?0(,1(,2)?)?$
+
+
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+ 'ms_index' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'
+
+
+ 'parameter.txt' in outputs_selected
+
+
+
+ 'psm.txt' in outputs_selected
+
+
+
+
+
+
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+ 'psm_rank.txt' in outputs_selected
+
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+ 'psm_rank.mgf' in outputs_selected
+
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+ 'psm_type.txt' in outputs_selected
+
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+ 'psm_annotation.txt' in outputs_selected
+
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+ 'detail.txt' in outputs_selected
+
+
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+ 'ptm.txt' in outputs_selected
+
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+ 'ptm_detail.txt' in outputs_selected
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