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comparison mashmap.xml @ 7:53f601fb8664 draft

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planemo upload
author fubar
date Sat, 24 Feb 2024 04:32:36 +0000
parents 27df186d5446
children 9ba0184870ef
comparison
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6:27df186d5446 7:53f601fb8664
1 <tool name="mashmap" id="mashmap" version="3.1.3" profile="22.05"> 1 <tool name="mashmap" id="mashmap" version="1.19.2" profile="22.05">
2 <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay--> 2 <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
3 <!--Created by toolfactory@galaxy.org at 23/02/2024 21:34:16 using the Galaxy Tool Factory.--> 3 <!--Created by toolfactory@galaxy.org at 24/02/2024 15:30:44 using the Galaxy Tool Factory.-->
4 <description>Fast local alignment boundaries</description> 4 <description>Fast local alignment boundaries</description>
5 <requirements> 5 <requirements>
6 <requirement version="3.1.3" type="package">mashmap</requirement> 6 <requirement version="3.1.3" type="package">mashmap</requirement>
7 <requirement version="1.19.2" type="package">samtools</requirement>
7 </requirements> 8 </requirements>
8 <version_command><![CDATA[echo "3.1.3"]]></version_command> 9 <version_command><![CDATA[echo "1.19.2"]]></version_command>
9 <command><![CDATA[bash '$runme']]></command> 10 <command><![CDATA[bash '$runme']]></command>
10 <configfiles> 11 <configfiles>
11 <configfile name="runme"><![CDATA[#if len($reflist) > 1: 12 <configfile name="runme"><![CDATA[#if len($reflist) > 1:
12 #for i, mash in enumerate($reflist): 13 #for i, mash in enumerate($reflist):
13 #if i == 0: 14 #if i == 0:
15 #else: 16 #else:
16 echo '$mash' >> 'reflist' && 17 echo '$mash' >> 'reflist' &&
17 #end if 18 #end if
18 #end for 19 #end for
19 #end if 20 #end if
21 samtools faidx '$query' &&
20 mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' $dense \ 22 mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' $dense \
21 #if int($sketchSize) > 0: 23 #if int($sketchSize) > 0:
22 -J '$sketchSize' \ 24 -J '$sketchSize' \
23 #end if 25 #end if
24 #if len($reflist) == 1: 26 #if len($reflist) == 1:
68 70
69 Map set of query sequences against a reference genome: 71 Map set of query sequences against a reference genome:
70 72
71 mashmap -r reference.fna -q query.fa 73 mashmap -r reference.fna -q query.fa
72 74
73 The output is a paf format file (https://github.com/lh3/miniasm/blob/master/PAF.md). 75 The output is space-delimited with each line consisting of query name, length, 0-based start, end, strand, target name, length, start, end and mapping nucleotide identity.
74 Thi is space-delimited with each line consisting of query name, length, 0-based start, end, strand, target name, length, start, end and mapping nucleotide identity.
75 76
76 Map set of query seqences against a list of reference genomes: 77 Map set of query seqences against a list of reference genomes:
77 78
78 mashmap --rl referenceList.txt -q query.fa 79 mashmap --rl referenceList.txt -q query.fa
79 80