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comparison mashmap.xml @ 9:dc53eb4354a6 draft

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planemo upload
author fubar
date Sat, 24 Feb 2024 08:20:07 +0000
parents 9ba0184870ef
children 08a74c1a4562
comparison
equal deleted inserted replaced
8:9ba0184870ef 9:dc53eb4354a6
1 <tool name="mashmap" id="mashmap" version="1.19.2" 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 24/02/2024 15:58:22 using the Galaxy Tool Factory.--> 3 <!--Created by toolfactory@galaxy.org at 24/02/2024 19:18:09 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 <requirement version="1.19.2" type="package">samtools</requirement>
8 </requirements> 8 </requirements>
9 <version_command><![CDATA[echo "1.19.2"]]></version_command> 9 <version_command><![CDATA[echo "1.19.2"]]></version_command>
10 <command><![CDATA[bash '$runme']]></command> 10 <command><![CDATA[bash '$runme']]></command>
11 <configfiles> 11 <configfiles>
12 <configfile name="runme"><![CDATA[#if len($reflist) > 1: 12 <configfile name="runme"><![CDATA[ln -s '$query' 'query' &&
13 #if len($reflist) > 1:
13 #for i, mash in enumerate($reflist): 14 #for i, mash in enumerate($reflist):
14 #if i == 0: 15 #if i == 0:
15 echo '$mash' > 'reflist' && 16 echo '$mash' > 'reflist' &&
16 #else: 17 #else:
17 echo '$mash' >> 'reflist' && 18 echo '$mash' >> 'reflist' &&
18 #end if 19 #end if
19 #end for 20 #end for
20 #end if 21 #end if
21 samtools faidx '$query' && 22 samtools faidx 'query' &&
22 mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' $dense \ 23 mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' $dense \
23 #if int($sketchSize) > 0: 24 #if int($sketchSize) > 0:
24 -J '$sketchSize' \ 25 -J '$sketchSize' \
25 #end if 26 #end if
26 #if len($reflist) == 1: 27 #if len($reflist) == 1:
27 -r '$reflist' -q '$query' && 28 -r '$reflist' -q 'query' &&
28 #else 29 #else
29 --rl 'reflist' -q '$query' && 30 --rl 'reflist' -q 'query' &&
30 #end if 31 #end if
31 cp 'mashmap.out' '$mashout']]></configfile> 32 cp 'mashmap.out' '$mashout']]></configfile>
32 </configfiles> 33 </configfiles>
33 <inputs> 34 <inputs>
34 <param name="query" type="data" optional="false" label="Query sequences (as fasta) to mash against the references supplied below" help="" format="fasta" multiple="false"/> 35 <param name="query" type="data" optional="false" label="Query sequences (as fasta) to mash against the references supplied below" help="" format="fasta" multiple="false"/>