Mercurial > repos > dnbenso > masurca_simple

comparison masurca_simple.xml @ 1:86aa445e75d6 draft default tip

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author dnbenso
date Fri, 28 Jan 2022 04:19:38 +0000
parents 0a33488ca043
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0:0a33488ca043 1:86aa445e75d6
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 #set $long = 'false' 10 #set $long = 'false'
11 #if $nanopore_input.np_input == "Yes": 11 #if $nanopore_input.np_input == "Yes":
12 #if $pacbio_input.pb_input == "Yes": 12 #if $pacbio_input.pb_input == "Yes":
13 cat '$nanopore_input.nano' '$pacbio_input.pacbio' > long.fastq.gz && 13 cat '$nanopore_input.nano' '$pacbio_input.pacbio' > \$_GALAXY_JOB_TMP_DIR/long.fastq.gz &&
14 #else: 14 #else:
15 ln -s '$nanopore_input.nano' long.fastq.gz && 15 ln -s '$nanopore_input.nano' \$_GALAXY_JOB_TMP_DIR/long.fastq.gz &&
16 #end if 16 #end if
17 #set $long = 'true' 17 #set $long = 'true'
18 #elif $pacbio_input.pb_input == "Yes": 18 #elif $pacbio_input.pb_input == "Yes":
19 ln -s '$pacbio_input.pacbio' long.fastq.gz && 19 ln -s '$pacbio_input.pacbio' \$_GALAXY_JOB_TMP_DIR/long.fastq.gz &&
20 #set $long = 'true' 20 #set $long = 'true'
21 #end if 21 #end if
22 masurca -t \${GALAXY_SLOTS:-8} -i 22 masurca -t \${GALAXY_SLOTS:-8} -i
23 #if str( $illumina_input.input_type ) == "single" 23 #if str( $illumina_input.input_type ) == "single"
24 '$illumina_input.fastq_input1' 24 '$illumina_input.fastq_input1'
26 '$illumina_input.fastq_input1','$illumina_input.fastq_input2' 26 '$illumina_input.fastq_input1','$illumina_input.fastq_input2'
27 #elif str( $illumina_input.input_type ) == "paired_collection" 27 #elif str( $illumina_input.input_type ) == "paired_collection"
28 '$illumina_input.fastq_input1','$illumina_input.fastq_input2' 28 '$illumina_input.fastq_input1','$illumina_input.fastq_input2'
29 #end if 29 #end if
30 #if $long == "true": 30 #if $long == "true":
31 -r long.fastq.gz 31 -r \$_GALAXY_JOB_TMP_DIR/long.fastq.gz
32 #end if 32 #end if
33 ]]></command> 33 ]]></command>
34 <inputs> 34 <inputs>
35 <conditional name="illumina_input"> 35 <conditional name="illumina_input">
36 <param name="input_type" type="select" label="Paired-end reads" help="Select between paired and paired collection"> 36 <param name="input_type" type="select" label="Paired-end reads" help="Select between paired and paired collection">
90 <param name="nano" value="onp.fa"/> 90 <param name="nano" value="onp.fa"/>
91 </conditional> 91 </conditional>
92 <conditional name="pacbio_input"> 92 <conditional name="pacbio_input">
93 <param name="pb_input" value="No" /> 93 <param name="pb_input" value="No" />
94 </conditional> 94 </conditional>
95 <output name="superReads" ftype="fasta" /> 95 <output name="superReads" ftype="fasta">
96 <assert_contents>
97 <has_line_matching expression="^TCCGAAAGTGTTAACTT.*"/>
98 </assert_contents>
99 </output>
96 </test> 100 </test>
97 </tests> 101 </tests>
98 <help><![CDATA[ 102 <help><![CDATA[
99 103
100 This implementation of MaSuRCA is for small projects that only have PE 104 This implementation of MaSuRCA is for small projects that only have PE