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comparison bowtie_wrapper.xml @ 2:ba29251df197 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit b2e1043bf4db38be490fec298a1829f8e4a1c48e
author devteam
date Thu, 18 Aug 2016 10:19:58 -0400
parents 867a8c8e870e
children 9326d6e6882a
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1:867a8c8e870e 2:ba29251df197
1 <tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.4"> 1 <tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.5">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.12.7">bowtie</requirement> 3 <requirement type="package" version="1.1.2">bowtie</requirement>
4 </requirements> 4 </requirements>
5 <description></description> 5 <description></description>
6 <version_command>bowtie --version</version_command> 6 <version_command>bowtie --version</version_command>
7 <command interpreter="python"> 7 <command interpreter="python">
8 bowtie_wrapper.py 8 bowtie_wrapper.py
550 <param name="index" value="equCab2chrM" /> 550 <param name="index" value="equCab2chrM" />
551 <param name="sPaired" value="single" /> 551 <param name="sPaired" value="single" />
552 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /> 552 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
553 <param name="sSettingsType" value="preSet" /> 553 <param name="sSettingsType" value="preSet" />
554 <param name="suppressHeader" value="true" /> 554 <param name="suppressHeader" value="true" />
555 <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True" /> 555 <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True">
556 <metadata name="dbkey" value="equCab2" />
557 </output>
556 </test> 558 </test>
557 <test> 559 <test>
558 <!-- 560 <!--
559 Bowtie command: 561 Bowtie command:
560 bowtie-build -f test-data/phiX.fasta phiX_base 562 bowtie-build -f test-data/phiX.fasta phiX_base
718 <param name="sMaxFile" value="false" /> 720 <param name="sMaxFile" value="false" />
719 <param name="sBest" value="noBest" /> 721 <param name="sBest" value="noBest" />
720 <param name="sOffrate" value="-1" /> 722 <param name="sOffrate" value="-1" />
721 <param name="sSeed" value="-1" /> 723 <param name="sSeed" value="-1" />
722 <param name="suppressHeader" value="true" /> 724 <param name="suppressHeader" value="true" />
723 <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True" /> 725 <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True">
726 <metadata name="dbkey" value="equCab2" />
727 </output>
724 </test> 728 </test>
725 <test> 729 <test>
726 <!-- 730 <!--
727 Bowtie command: 731 Bowtie command:
728 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base 732 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base