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annotate 1_map_reads.xml @ 62:d497922d6caa

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author jpayne
date Fri, 28 Jun 2024 00:26:24 -0400
parents 2af5e948dd5c
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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@62 4 <container type="docker">quay.io/staphb/cfsan-snp-pipeline</container>
jpayne@62 5 <!-- <requirement type="package" version="1.0.8">bzip2</requirement>
jpayne@58 6 <requirement type="package" version="2.4.5">bowtie2</requirement>
jpayne@62 7 <requirement type="package" version="1.9.134">boto3</requirement> -->
jpayne@58 8 <!-- <requirement type="package" version="3.6.8">python</requirement> -->
jpayne@0 9 </requirements>
jpayne@0 10 <command detect_errors="exit_code"><![CDATA[
jpayne@40 11 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
jpayne@0 12 #if $reads.reads_select == 'collection'
jpayne@44 13 #set forward=$reads.coll.forward
jpayne@44 14 #set reverse=$reads.coll.reverse
jpayne@0 15 #end if
jpayne@9 16 python ${__tool_directory__}/snp-cache.py snp_mapped_reads
jpayne@0 17 "\$(md5sum $reference
jpayne@44 18 $forward
jpayne@44 19 $reverse
jpayne@0 20 | cut -c -32 | md5sum | cut -c -32)"
jpayne@0 21 -c "
jpayne@0 22 cp $reference ./reference.fasta
jpayne@44 23 #if $forward.is_of_type("fastq.gz","fastqsanger.gz")
jpayne@44 24 && cp $forward ./forward.gz
jpayne@44 25 #set $forward="./forward.gz"
jpayne@44 26 #else if $forward.is_of_type("fastq.bz2", "fastqsanger.bz2")
jpayne@44 27 && cp $forward ./forward.bz2
jpayne@44 28 #set $forward="./forward.bz2"
jpayne@44 29 #end if
jpayne@44 30 #if $reverse.is_of_type("fastq.gz","fastqsanger.gz")
jpayne@44 31 && cp $reverse ./reverse.gz
jpayne@44 32 #set $reverse="./reverse.gz"
jpayne@44 33 #else if $reverse.is_of_type("fastq.bz2", "fastqsanger.bz2")
jpayne@44 34 && cp $reverse ./reverse.bz2
jpayne@44 35 #set $reverse="./reverse.bz2"
jpayne@44 36 #end if
jpayne@0 37 && bowtie2-build ./reference.fasta --quiet --threads \${GALAXY_SLOTS:-4} ./reference
jpayne@44 38 && bowtie2 -q -x ./reference -1 $forward -2 $reverse -p \${GALAXY_SLOTS:-4} --reorder -X 1000
jpayne@0 39 "
jpayne@0 40 #if $reads.reads_select == 'collection'
jpayne@0 41 -o ${align_from_collection}
jpayne@0 42 #else
jpayne@0 43 -o ${align_from_history}
jpayne@0 44 #end if
jpayne@0 45 -l $cache_log
jpayne@0 46 && cat $cache_log
jpayne@0 47 #if $source.source_select == 'curated'
jpayne@0 48 && cp $reference $ref_out
jpayne@0 49 #end if
jpayne@0 50 ]]></command>
jpayne@0 51 <inputs>
jpayne@0 52 <!-- <conditional name="source">
jpayne@0 53 <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 54 <option value="bioproject">Provide a BioProject</option>
jpayne@0 55 <option value="curated">Use a GalaxyTrakr reference</option>
jpayne@0 56 <option value="history">Use a reference from your history</option>
jpayne@0 57 </param>
jpayne@0 58 <when value="bioproject">
jpayne@0 59 <param type="data" name="bioproject" format="text" />
jpayne@0 60 </when>
jpayne@0 61 <when value="curated">
jpayne@0 62 <param name="input" type="select" label="Select reference fasta">
jpayne@0 63 <options from_data_table="all_fasta">
jpayne@0 64 <filter type="sort_by" column="2"/>
jpayne@0 65 <validator type="no_options" message="No assemblies are available for the selected input dataset"/>
jpayne@0 66 </options>
jpayne@0 67 </param>
jpayne@0 68 </when>
jpayne@0 69 <when value="history">
jpayne@0 70 <param type="data" name="input" format="fasta" label="Select reference FASTA"/>
jpayne@0 71 </when>
jpayne@0 72 </conditional> -->
jpayne@0 73 <conditional name="source">
jpayne@0 74 <param name="source_select" type="select" label="Use a curated GalaxyTrakr reference or a reference from your history">
jpayne@0 75 <option value="curated">Use a GalaxyTrakr reference</option>
jpayne@0 76 <option value="history">Use a reference from your history</option>
jpayne@0 77 </param>
jpayne@0 78 <when value="curated">
jpayne@0 79 <param name="reference" type="select" label="Select reference fasta">
jpayne@0 80 <options from_data_table="all_fasta">
jpayne@0 81 <filter type="sort_by" column="2"/>
jpayne@0 82 <validator type="no_options" message="No assemblies are available for the selected input dataset"/>
jpayne@0 83 </options>
jpayne@0 84 </param>
jpayne@0 85 </when>
jpayne@0 86 <when value="history">
jpayne@0 87 <param type="data" name="reference" format="fasta" label="Select reference FASTA"/>
jpayne@0 88 </when>
jpayne@0 89 </conditional>
jpayne@0 90 <conditional name="reads">
jpayne@0 91 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
jpayne@0 92 <option value="collection">Paired collection from your history</option>
jpayne@0 93 <option value="history">Two FASTQ datasets from your history</option>
jpayne@0 94 </param>
jpayne@0 95 <when value="collection">
jpayne@44 96 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
jpayne@0 97 </when>
jpayne@0 98 <when value="history">
jpayne@44 99 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
jpayne@44 100 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
jpayne@0 101 </when>
jpayne@0 102 </conditional>
jpayne@0 103 </inputs>
jpayne@0 104 <outputs>
jpayne@0 105 <data label="${reads.coll.name} alignment" name="align_from_collection" format="sam">
jpayne@0 106 <filter>reads['reads_select'] == 'collection'</filter>
jpayne@0 107 </data>
jpayne@0 108 <data label="${reads.forward.name.split('_')[0]} alignment" name="align_from_history" format="sam">
jpayne@0 109 <filter>reads['reads_select'] == 'history'</filter>
jpayne@0 110 </data>
jpayne@0 111 <data label="S3 Cache log" name="cache_log" format="txt" hidden="true" />
jpayne@0 112 <data label="Reference" name="ref_out" format="fasta" hidden="true">
jpayne@0 113 <filter>source['source_select'] == curated</filter>
jpayne@0 114 </data>
jpayne@0 115 </outputs>
jpayne@0 116 <tests>
jpayne@0 117 <test>
jpayne@0 118 <param name="source_select" value="history" />
jpayne@0 119 <param name="reference" value="reference/lambda_virus.fasta" ftype="fasta" />
jpayne@0 120 <param name="reads_select" value="history" />
jpayne@0 121 <param name="forward" value="samples/sample1/sample1_1.fastq" ftype="fastqsanger" />
jpayne@0 122 <param name="reverse" value="samples/sample1/sample1_2.fastq" ftype="fastqsanger" />
jpayne@0 123 <output name="align_from_history" value="samples/sample1/reads.sam" lines_diff="3" />
jpayne@0 124 </test>
jpayne@0 125 <test>
jpayne@0 126 <param name="source_select" value="history" />
jpayne@0 127 <param name="reference" value="reference/lambda_virus.fasta" ftype="fasta" />
jpayne@0 128 <param name="reads_select" value="collection" />
jpayne@0 129 <param name="coll">
jpayne@0 130 <collection type="paired">
jpayne@0 131 <element name="forward" value="samples/sample1/sample1_1.fastq" ftype="fastqsanger" />
jpayne@0 132 <element name="reverse" value="samples/sample1/sample1_2.fastq" ftype="fastqsanger" />
jpayne@0 133 </collection>
jpayne@0 134 </param>
jpayne@0 135 <output name="align_from_collection" value="samples/sample1/reads.sam" lines_diff="3" />
jpayne@0 136 </test>
jpayne@44 137 <test>
jpayne@44 138 <param name="source_select" value="history" />
jpayne@44 139 <param name="reference" value="reference/lambda_virus.fasta" ftype="fasta" />
jpayne@44 140 <param name="reads_select" value="history" />
jpayne@44 141 <param name="forward" value="samples/sample1/sample1_1.fastq.gz" ftype="fastqsanger.gz" />
jpayne@44 142 <param name="reverse" value="samples/sample1/sample1_2.fastq.gz" ftype="fastqsanger.gz" />
jpayne@44 143 <output name="align_from_history" value="samples/sample1/reads.sam" lines_diff="3" />
jpayne@44 144 </test>
jpayne@0 145 </tests>
jpayne@0 146 <help><![CDATA[
jpayne@0 147 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
jpayne@0 148 ]]></help>
jpayne@0 149 <citations>
jpayne@0 150 <citation type="doi">10.7717/peerj-cs.20</citation>
jpayne@0 151 <!-- <citation type="bibtex">
jpayne@0 152 @misc{cfsan-snp-pipeline,
jpayne@0 153 author = {Steve Davis and James Pettengill and Yan Luo and Justin Payne and Albert Shpuntoff and Rugh Rand and Errol Strain},
jpayne@0 154 year = {2015},
jpayne@0 155 title = {CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data},
jpayne@0 156 url = {https://doi.org/10.7717/peerj-cs.20},
jpayne@0 157 journal = {PeerJ Computer Science},
jpayne@0 158 }</citation> -->
jpayne@0 159 </citations>
jpayne@0 160 </tool>