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comparison bowtie_wrapper.xml @ 1:867a8c8e870e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author devteam
date Fri, 18 Dec 2015 18:50:53 -0500
parents 4926b3e1e2fe
children ba29251df197
comparison
equal deleted inserted replaced
0:4926b3e1e2fe 1:867a8c8e870e
1 <tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.3"> 1 <tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.4">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.12.7">bowtie</requirement> 3 <requirement type="package" version="0.12.7">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>
146 #end if 146 #end if
147 --offrate="${singlePaired.pParams.pOffrate}" 147 --offrate="${singlePaired.pParams.pOffrate}"
148 --seed="${singlePaired.pParams.pSeed}" 148 --seed="${singlePaired.pParams.pSeed}"
149 #end if 149 #end if
150 #end if 150 #end if
151 #if $save_mapping_stats
152 --output_mapping_stats="$mapping_stats"
153 #end if
151 </command> 154 </command>
152 <inputs> 155 <inputs>
153 <conditional name="refGenomeSource"> 156 <conditional name="refGenomeSource">
154 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> 157 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
155 <option value="indexed">Use a built-in index</option> 158 <option value="indexed">Use a built-in index</option>
413 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> 416 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
414 </when> <!-- full --> 417 </when> <!-- full -->
415 </conditional> <!-- pParams --> 418 </conditional> <!-- pParams -->
416 </when> <!-- paired --> 419 </when> <!-- paired -->
417 </conditional> <!-- singlePaired --> 420 </conditional> <!-- singlePaired -->
421 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie mapping statistics to the history" />
418 <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" /> 422 <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" />
419 </inputs> 423 </inputs>
420 <outputs> 424 <outputs>
421 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> 425 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
422 <actions> 426 <actions>
434 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> 438 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
435 </action> 439 </action>
436 </when> 440 </when>
437 </conditional> 441 </conditional>
438 </actions> 442 </actions>
443 </data>
444 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
445 <filter>save_mapping_stats is True</filter>
439 </data> 446 </data>
440 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)"> 447 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
441 <filter>(( 448 <filter>((
442 singlePaired['sPaired'] == "single" and 449 singlePaired['sPaired'] == "single" and
443 singlePaired['sParams']['sSettingsType'] == "full" and 450 singlePaired['sParams']['sSettingsType'] == "full" and
742 <param name="pMateOrient" value="ff" /> 749 <param name="pMateOrient" value="ff" />
743 <param name="pSettingsType" value="preSet" /> 750 <param name="pSettingsType" value="preSet" />
744 <param name="suppressHeader" value="true" /> 751 <param name="suppressHeader" value="true" />
745 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" /> 752 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
746 </test> 753 </test>
754 <test>
755 <!--
756 Bowtie command:
757 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
758 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam
759 sort bowtie_out10_u.sam > bowtie_out10.sam
760 -p is the number of threads. You need to replace the + with 2 dashes.
761 chrM_base is the index files' location/base name.
762 -->
763 <param name="genomeSource" value="history" />
764 <param name="ownFile" value="phiX.fasta" />
765 <param name="indexSettings" value="indexFull" />
766 <param name="autoB" value="auto" />
767 <param name="nodc" value="dc" />
768 <param name="noref" value="ref" />
769 <param name="offrate" value="5" />
770 <param name="ftab" value="10" />
771 <param name="ntoa" value="no" />
772 <param name="endian" value="little" />
773 <param name="seed" value="-1" />
774 <param name="sPaired" value="paired" />
775 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
776 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
777 <param name="pMaxInsert" value="1000" />
778 <param name="pMateOrient" value="ff" />
779 <param name="pSettingsType" value="preSet" />
780 <param name="suppressHeader" value="true" />
781 <param name="save_mapping_stats" value="true" />
782 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
783 <output name="mapping_stats" ftype="txt" file="bowtie_out11.txt" sort="True" />
784 </test>
747 </tests> 785 </tests>
748 786
749 <help> 787 <help>
750 788
751 **What it does** 789 **What it does**