Mercurial > repos > devteam > bowtie_wrappers
comparison bowtie_wrapper.xml @ 5:306077e393d4 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit b2e1043bf4db38be490fec298a1829f8e4a1c48e
author | devteam |
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date | Thu, 18 Aug 2016 10:20:09 -0400 |
parents | df86f29bedee |
children | ecbbc8be6266 |
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4:df86f29bedee | 5:306077e393d4 |
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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="1.1.5"> |
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 |
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 |
543 <param name="index" value="equCab2chrM" /> | 550 <param name="index" value="equCab2chrM" /> |
544 <param name="sPaired" value="single" /> | 551 <param name="sPaired" value="single" /> |
545 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /> | 552 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /> |
546 <param name="sSettingsType" value="preSet" /> | 553 <param name="sSettingsType" value="preSet" /> |
547 <param name="suppressHeader" value="true" /> | 554 <param name="suppressHeader" value="true" /> |
548 <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> | |
549 </test> | 558 </test> |
550 <test> | 559 <test> |
551 <!-- | 560 <!-- |
552 Bowtie command: | 561 Bowtie command: |
553 bowtie-build -f test-data/phiX.fasta phiX_base | 562 bowtie-build -f test-data/phiX.fasta phiX_base |
711 <param name="sMaxFile" value="false" /> | 720 <param name="sMaxFile" value="false" /> |
712 <param name="sBest" value="noBest" /> | 721 <param name="sBest" value="noBest" /> |
713 <param name="sOffrate" value="-1" /> | 722 <param name="sOffrate" value="-1" /> |
714 <param name="sSeed" value="-1" /> | 723 <param name="sSeed" value="-1" /> |
715 <param name="suppressHeader" value="true" /> | 724 <param name="suppressHeader" value="true" /> |
716 <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> | |
717 </test> | 728 </test> |
718 <test> | 729 <test> |
719 <!-- | 730 <!-- |
720 Bowtie command: | 731 Bowtie command: |
721 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 |
741 <param name="pMaxInsert" value="1000" /> | 752 <param name="pMaxInsert" value="1000" /> |
742 <param name="pMateOrient" value="ff" /> | 753 <param name="pMateOrient" value="ff" /> |
743 <param name="pSettingsType" value="preSet" /> | 754 <param name="pSettingsType" value="preSet" /> |
744 <param name="suppressHeader" value="true" /> | 755 <param name="suppressHeader" value="true" /> |
745 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" /> | 756 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" /> |
757 </test> | |
758 <test> | |
759 <!-- | |
760 Bowtie command: | |
761 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base | |
762 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 | |
763 sort bowtie_out10_u.sam > bowtie_out10.sam | |
764 -p is the number of threads. You need to replace the + with 2 dashes. | |
765 chrM_base is the index files' location/base name. | |
766 --> | |
767 <param name="genomeSource" value="history" /> | |
768 <param name="ownFile" value="phiX.fasta" /> | |
769 <param name="indexSettings" value="indexFull" /> | |
770 <param name="autoB" value="auto" /> | |
771 <param name="nodc" value="dc" /> | |
772 <param name="noref" value="ref" /> | |
773 <param name="offrate" value="5" /> | |
774 <param name="ftab" value="10" /> | |
775 <param name="ntoa" value="no" /> | |
776 <param name="endian" value="little" /> | |
777 <param name="seed" value="-1" /> | |
778 <param name="sPaired" value="paired" /> | |
779 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" /> | |
780 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" /> | |
781 <param name="pMaxInsert" value="1000" /> | |
782 <param name="pMateOrient" value="ff" /> | |
783 <param name="pSettingsType" value="preSet" /> | |
784 <param name="suppressHeader" value="true" /> | |
785 <param name="save_mapping_stats" value="true" /> | |
786 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" /> | |
787 <output name="mapping_stats" ftype="txt" file="bowtie_out11.txt" sort="True" /> | |
746 </test> | 788 </test> |
747 </tests> | 789 </tests> |
748 | 790 |
749 <help> | 791 <help> |
750 | 792 |