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comparison 1_map_reads.xml @ 44:e7cac7790476

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planemo upload commit 0399c6bd696435a7a99d8d8b4c237e5a78ee5856-dirty
author jpayne
date Wed, 25 Apr 2018 16:35:27 -0400
parents 62531f7399dc
children f58616a4b2f3
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43:62531f7399dc 44:e7cac7790476
7 <!-- <requirement type="package" version="3.5">python</requirement> --> 7 <!-- <requirement type="package" version="3.5">python</requirement> -->
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && 10 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
11 #if $reads.reads_select == 'collection' 11 #if $reads.reads_select == 'collection'
12 export files="$reads.coll.forward $reads.coll.reverse" && 12 #set forward=$reads.coll.forward
13 export params="-1 $reads.coll.forward -2 $reads.coll.reverse" && 13 #set reverse=$reads.coll.reverse
14 #else
15 export files="$forward $reverse" &&
16 export params="-1 $forward -2 $reverse" &&
17 #end if 14 #end if
18 python ${__tool_directory__}/snp-cache.py snp_mapped_reads 15 python ${__tool_directory__}/snp-cache.py snp_mapped_reads
19 "\$(md5sum $reference 16 "\$(md5sum $reference
20 \$files 17 $forward
18 $reverse
21 | cut -c -32 | md5sum | cut -c -32)" 19 | cut -c -32 | md5sum | cut -c -32)"
22 -c " 20 -c "
23 cp $reference ./reference.fasta 21 cp $reference ./reference.fasta
22 #if $forward.is_of_type("fastq.gz","fastqsanger.gz")
23 && cp $forward ./forward.gz
24 #set $forward="./forward.gz"
25 #else if $forward.is_of_type("fastq.bz2", "fastqsanger.bz2")
26 && cp $forward ./forward.bz2
27 #set $forward="./forward.bz2"
28 #end if
29 #if $reverse.is_of_type("fastq.gz","fastqsanger.gz")
30 && cp $reverse ./reverse.gz
31 #set $reverse="./reverse.gz"
32 #else if $reverse.is_of_type("fastq.bz2", "fastqsanger.bz2")
33 && cp $reverse ./reverse.bz2
34 #set $reverse="./reverse.bz2"
35 #end if
24 && bowtie2-build ./reference.fasta --quiet --threads \${GALAXY_SLOTS:-4} ./reference 36 && bowtie2-build ./reference.fasta --quiet --threads \${GALAXY_SLOTS:-4} ./reference
25 && bowtie2 -q -x ./reference \$params -p \${GALAXY_SLOTS:-4} --reorder -X 1000 37 && bowtie2 -q -x ./reference -1 $forward -2 $reverse -p \${GALAXY_SLOTS:-4} --reorder -X 1000
26 " 38 "
27 #if $reads.reads_select == 'collection' 39 #if $reads.reads_select == 'collection'
28 -o ${align_from_collection} 40 -o ${align_from_collection}
29 #else 41 #else
30 -o ${align_from_history} 42 -o ${align_from_history}
78 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history"> 90 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
79 <option value="collection">Paired collection from your history</option> 91 <option value="collection">Paired collection from your history</option>
80 <option value="history">Two FASTQ datasets from your history</option> 92 <option value="history">Two FASTQ datasets from your history</option>
81 </param> 93 </param>
82 <when value="collection"> 94 <when value="collection">
83 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" /> 95 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
84 </when> 96 </when>
85 <when value="history"> 97 <when value="history">
86 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" /> 98 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
87 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" /> 99 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
88 </when> 100 </when>
89 </conditional> 101 </conditional>
90 </inputs> 102 </inputs>
91 <outputs> 103 <outputs>
92 <data label="${reads.coll.name} alignment" name="align_from_collection" format="sam"> 104 <data label="${reads.coll.name} alignment" name="align_from_collection" format="sam">
119 <element name="reverse" value="samples/sample1/sample1_2.fastq" ftype="fastqsanger" /> 131 <element name="reverse" value="samples/sample1/sample1_2.fastq" ftype="fastqsanger" />
120 </collection> 132 </collection>
121 </param> 133 </param>
122 <output name="align_from_collection" value="samples/sample1/reads.sam" lines_diff="3" /> 134 <output name="align_from_collection" value="samples/sample1/reads.sam" lines_diff="3" />
123 </test> 135 </test>
136 <test>
137 <param name="source_select" value="history" />
138 <param name="reference" value="reference/lambda_virus.fasta" ftype="fasta" />
139 <param name="reads_select" value="history" />
140 <param name="forward" value="samples/sample1/sample1_1.fastq.gz" ftype="fastqsanger.gz" />
141 <param name="reverse" value="samples/sample1/sample1_2.fastq.gz" ftype="fastqsanger.gz" />
142 <output name="align_from_history" value="samples/sample1/reads.sam" lines_diff="3" />
143 </test>
124 </tests> 144 </tests>
125 <help><![CDATA[ 145 <help><![CDATA[
126 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a> 146 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
127 ]]></help> 147 ]]></help>
128 <citations> 148 <citations>