Mercurial > repos > fubar > mashmap
comparison mashmap.xml @ 5:10e4181a6443 draft
planemo upload
| author | fubar |
|---|---|
| date | Fri, 23 Feb 2024 09:59:25 +0000 |
| parents | fba99cb9b0ef |
| children | 27df186d5446 |
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| 4:fba99cb9b0ef | 5:10e4181a6443 |
|---|---|
| 1 <tool name="mashmap" id="mashmap" version="3.1.3" profile="22.05"> | 1 <tool name="mashmap" id="mashmap" version="3.1.3" 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 20:28:46 using the Galaxy Tool Factory.--> | 3 <!--Created by toolfactory@galaxy.org at 23/02/2024 20:50:55 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 </requirements> | 7 </requirements> |
| 8 <version_command><![CDATA[echo "3.1.3"]]></version_command> | 8 <version_command><![CDATA[echo "3.1.3"]]></version_command> |
| 9 <command><![CDATA[bash '$runme']]></command> | 9 <command><![CDATA[bash '$runme']]></command> |
| 10 <configfiles> | 10 <configfiles> |
| 11 <configfile name="runme"><![CDATA[mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' $dense \ | 11 <configfile name="runme"><![CDATA[#if len($reflist) > 1: |
| 12 #for i, mash in enumerate($reflist): | |
| 13 #if i == 0: | |
| 14 echo $mash > 'reflist' && | |
| 15 #else: | |
| 16 echo $mash >> 'reflist' && | |
| 17 #end if | |
| 18 #end for | |
| 19 #end if | |
| 20 mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' $dense \ | |
| 12 #if int($sketchSize) > 0: | 21 #if int($sketchSize) > 0: |
| 13 -J '$sketchSize' \ | 22 -J '$sketchSize' \ |
| 14 #end if | 23 #end if |
| 15 #if len($reflist) == 1: | 24 #if len($reflist) == 1: |
| 16 -r $reflist -q '$query' | 25 -r $reflist -q '$query' && |
| 17 #else | 26 #else |
| 18 #for i, mash in enumerate($reflist): | 27 --rl 'reflist' -q '$query' && |
| 19 #if i == 0: | |
| 20 echo $mash > 'reflist' | |
| 21 #else: | |
| 22 echo $mash >> 'reflist' | |
| 23 #end if | |
| 24 #end for | |
| 25 --rl 'reflist' -q '$query' | |
| 26 #end if | 28 #end if |
| 27 cp 'mashmap.out' $mashout]]></configfile> | 29 cp 'mashmap.out' $mashout]]></configfile> |
| 28 </configfiles> | 30 </configfiles> |
| 29 <inputs> | 31 <inputs> |
| 30 <param name="query" type="data" optional="false" label="Query sequences (as fasta) to mash against the references supplied below" help="" format="fasta" multiple="false"/> | 32 <param name="query" type="data" optional="false" label="Query sequences (as fasta) to mash against the references supplied below" help="" format="fasta" multiple="false"/> |