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annotate 1_map_reads.xml @ 0:eefdd97a6749

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planemo upload commit b'7f6183b769772449fbcee903686b8d5ec5b7439f\n'-dirty
author jpayne
date Wed, 24 Jan 2018 14:18:21 -0500
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children 62191abf5426
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jpayne@0 1 <tool id="map_reads" name="1. Map Reads" version="1.0.1" profile="16.10">
jpayne@0 2 <description>to index, or lookup cached alignment</description>
jpayne@0 3 <requirements>
jpayne@0 4 <requirement type="package" version="2.3.4">bowtie2</requirement>
jpayne@0 5 <requirement type="package" version="1.5.11">boto3</requirement>
jpayne@0 6 </requirements>
jpayne@0 7 <command detect_errors="exit_code"><![CDATA[
jpayne@0 8 #if $reads.reads_select == 'collection'
jpayne@0 9 export files="$reads.coll.forward $reads.coll.reverse" &&
jpayne@0 10 export params="-1 $reads.coll.forward -2 $reads.coll.reverse" &&
jpayne@0 11 #else
jpayne@0 12 export files="$forward $reverse" &&
jpayne@0 13 export params="-1 $forward -2 $reverse" &&
jpayne@0 14 #end if
jpayne@0 15 ${__tool_directory__}/snp-cache.py snp_mapped_reads
jpayne@0 16 "\$(md5sum $reference
jpayne@0 17 \$files
jpayne@0 18 | cut -c -32 | md5sum | cut -c -32)"
jpayne@0 19 -c "
jpayne@0 20 cp $reference ./reference.fasta
jpayne@0 21 && bowtie2-build ./reference.fasta --quiet --threads \${GALAXY_SLOTS:-4} ./reference
jpayne@0 22 && bowtie2 -q -x ./reference \$params -p \${GALAXY_SLOTS:-4} --reorder -X 1000
jpayne@0 23 "
jpayne@0 24 #if $reads.reads_select == 'collection'
jpayne@0 25 -o ${align_from_collection}
jpayne@0 26 #else
jpayne@0 27 -o ${align_from_history}
jpayne@0 28 #end if
jpayne@0 29 -l $cache_log
jpayne@0 30 && cat $cache_log
jpayne@0 31 #if $source.source_select == 'curated'
jpayne@0 32 && cp $reference $ref_out
jpayne@0 33 #end if
jpayne@0 34 ]]></command>
jpayne@0 35 <inputs>
jpayne@0 36 <!-- <conditional name="source">
jpayne@0 37 <param name="source_select" type="select" label="Use the reference associated with a provided BioProject, a curated GalaxyTrakr reference, or a reference from your history">
jpayne@0 38 <option value="bioproject">Provide a BioProject</option>
jpayne@0 39 <option value="curated">Use a GalaxyTrakr reference</option>
jpayne@0 40 <option value="history">Use a reference from your history</option>
jpayne@0 41 </param>
jpayne@0 42 <when value="bioproject">
jpayne@0 43 <param type="data" name="bioproject" format="text" />
jpayne@0 44 </when>
jpayne@0 45 <when value="curated">
jpayne@0 46 <param name="input" type="select" label="Select reference fasta">
jpayne@0 47 <options from_data_table="all_fasta">
jpayne@0 48 <filter type="sort_by" column="2"/>
jpayne@0 49 <validator type="no_options" message="No assemblies are available for the selected input dataset"/>
jpayne@0 50 </options>
jpayne@0 51 </param>
jpayne@0 52 </when>
jpayne@0 53 <when value="history">
jpayne@0 54 <param type="data" name="input" format="fasta" label="Select reference FASTA"/>
jpayne@0 55 </when>
jpayne@0 56 </conditional> -->
jpayne@0 57 <conditional name="source">
jpayne@0 58 <param name="source_select" type="select" label="Use a curated GalaxyTrakr reference or a reference from your history">
jpayne@0 59 <option value="curated">Use a GalaxyTrakr reference</option>
jpayne@0 60 <option value="history">Use a reference from your history</option>
jpayne@0 61 </param>
jpayne@0 62 <when value="curated">
jpayne@0 63 <param name="reference" type="select" label="Select reference fasta">
jpayne@0 64 <options from_data_table="all_fasta">
jpayne@0 65 <filter type="sort_by" column="2"/>
jpayne@0 66 <validator type="no_options" message="No assemblies are available for the selected input dataset"/>
jpayne@0 67 </options>
jpayne@0 68 </param>
jpayne@0 69 </when>
jpayne@0 70 <when value="history">
jpayne@0 71 <param type="data" name="reference" format="fasta" label="Select reference FASTA"/>
jpayne@0 72 </when>
jpayne@0 73 </conditional>
jpayne@0 74 <conditional name="reads">
jpayne@0 75 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
jpayne@0 76 <option value="collection">Paired collection from your history</option>
jpayne@0 77 <option value="history">Two FASTQ datasets from your history</option>
jpayne@0 78 </param>
jpayne@0 79 <when value="collection">
jpayne@0 80 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger" collection_type="paired" />
jpayne@0 81 </when>
jpayne@0 82 <when value="history">
jpayne@0 83 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger" />
jpayne@0 84 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger" />
jpayne@0 85 </when>
jpayne@0 86 </conditional>
jpayne@0 87 </inputs>
jpayne@0 88 <outputs>
jpayne@0 89 <data label="${reads.coll.name} alignment" name="align_from_collection" format="sam">
jpayne@0 90 <filter>reads['reads_select'] == 'collection'</filter>
jpayne@0 91 </data>
jpayne@0 92 <data label="${reads.forward.name.split('_')[0]} alignment" name="align_from_history" format="sam">
jpayne@0 93 <filter>reads['reads_select'] == 'history'</filter>
jpayne@0 94 </data>
jpayne@0 95 <data label="S3 Cache log" name="cache_log" format="txt" hidden="true" />
jpayne@0 96 <data label="Reference" name="ref_out" format="fasta" hidden="true">
jpayne@0 97 <filter>source['source_select'] == curated</filter>
jpayne@0 98 </data>
jpayne@0 99 </outputs>
jpayne@0 100 <tests>
jpayne@0 101 <test>
jpayne@0 102 <param name="source_select" value="history" />
jpayne@0 103 <param name="reference" value="reference/lambda_virus.fasta" ftype="fasta" />
jpayne@0 104 <param name="reads_select" value="history" />
jpayne@0 105 <param name="forward" value="samples/sample1/sample1_1.fastq" ftype="fastqsanger" />
jpayne@0 106 <param name="reverse" value="samples/sample1/sample1_2.fastq" ftype="fastqsanger" />
jpayne@0 107 <output name="align_from_history" value="samples/sample1/reads.sam" lines_diff="3" />
jpayne@0 108 </test>
jpayne@0 109 <test>
jpayne@0 110 <param name="source_select" value="history" />
jpayne@0 111 <param name="reference" value="reference/lambda_virus.fasta" ftype="fasta" />
jpayne@0 112 <param name="reads_select" value="collection" />
jpayne@0 113 <param name="coll">
jpayne@0 114 <collection type="paired">
jpayne@0 115 <element name="forward" value="samples/sample1/sample1_1.fastq" ftype="fastqsanger" />
jpayne@0 116 <element name="reverse" value="samples/sample1/sample1_2.fastq" ftype="fastqsanger" />
jpayne@0 117 </collection>
jpayne@0 118 </param>
jpayne@0 119 <output name="align_from_collection" value="samples/sample1/reads.sam" lines_diff="3" />
jpayne@0 120 </test>
jpayne@0 121 </tests>
jpayne@0 122 <help><![CDATA[
jpayne@0 123 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
jpayne@0 124 ]]></help>
jpayne@0 125 <citations>
jpayne@0 126 <citation type="doi">10.7717/peerj-cs.20</citation>
jpayne@0 127 <!-- <citation type="bibtex">
jpayne@0 128 @misc{cfsan-snp-pipeline,
jpayne@0 129 author = {Steve Davis and James Pettengill and Yan Luo and Justin Payne and Albert Shpuntoff and Rugh Rand and Errol Strain},
jpayne@0 130 year = {2015},
jpayne@0 131 title = {CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data},
jpayne@0 132 url = {https://doi.org/10.7717/peerj-cs.20},
jpayne@0 133 journal = {PeerJ Computer Science},
jpayne@0 134 }</citation> -->
jpayne@0 135 </citations>
jpayne@0 136 </tool>