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comparison repenrich.xml @ 4:d1f7ab78f7b5 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 2066f507880250c0093e7353e7c18910c002b05f
author artbio
date Sun, 18 Nov 2018 12:53:01 -0500
parents 1c9810ba0638
children 02a8941da83b
comparison
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3:1c9810ba0638 4:d1f7ab78f7b5
1 <tool id="repenrich" name="RepEnrich" version="1.4.3"> 1 <tool id="repenrich" name="RepEnrich" version="1.5.0">
2 <description>Repeat Element Profiling</description> 2 <description>Repeat Element Profiling</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2.0">bowtie</requirement> 4 <requirement type="package" version="1.2.0">bowtie</requirement>
5 <requirement type="package" version="0.1.19">samtools</requirement> 5 <requirement type="package" version="0.1.19">samtools</requirement>
6 <requirement type="package" version="2.20.1">bedtools</requirement> 6 <requirement type="package" version="2.20.1">bedtools</requirement>
11 </stdio> 11 </stdio>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 #import re 13 #import re
14 #set input_base = 'Sample' 14 #set input_base = 'Sample'
15 #set baseReference = 'Genome' 15 #set baseReference = 'Genome'
16
17 ## uncompress fastq.gz or fastqsanger.gz if needed
18 #if $seq_method.seq_method_list == "single-read":
19 #if $input_fastq.is_of_type("fastq.gz", "fastqsanger.gz"):
20 gunzip < '$input_fastq' > '${input_base}.fastq' &&
21 #else:
22 ln -f -s '$input_fastq' '${input_base}.fastq' &&
23 #end if
24 #else:
25 #if $input2_fastq.is_of_type("fastq.gz", "fastqsanger.gz"):
26 gunzip < '$input_fastq' > '${input_base}.fastq' &&
27 gunzip < '$input2_fastq' > '${input_base}_2.fastq' &&
28 #else:
29 ln -f -s '$input_fastq' '${input_base}.fastq' &&
30 ln -f -s '$input2_fastq' '${input_base}_2.fastq' &&
31 #end if
32 #end if
33
16 ln -f -s '$genome' '${baseReference}.fa' && 34 ln -f -s '$genome' '${baseReference}.fa' &&
17 ln -f -s '$input_fastq' '${input_base}.fastq' &&
18 #if $seq_method.seq_method_list == "paired-end":
19 ln -f -s '$input2_fastq' '${input_base}_2.fastq' &&
20 #end if
21 bowtie-build '$genome' ${baseReference} && 35 bowtie-build '$genome' ${baseReference} &&
22 python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} && 36 python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} &&
23 #if $seq_method.seq_method_list == "single-read": 37 #if $seq_method.seq_method_list == "single-read":
24 bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt && 38 bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt &&
25 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) && 39 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) &&
93 <output name="bowtie_alignments" file="paired-aligned_reads.tab" ftype="tabular"/> 107 <output name="bowtie_alignments" file="paired-aligned_reads.tab" ftype="tabular"/>
94 <output name="class_fraction_counts" file="Samp-paired_class_fraction_counts.tab" ftype="tabular"/> 108 <output name="class_fraction_counts" file="Samp-paired_class_fraction_counts.tab" ftype="tabular"/>
95 <output name="family_fraction_counts" file="Samp-paired_family_fraction_counts.tab" ftype="tabular"/> 109 <output name="family_fraction_counts" file="Samp-paired_family_fraction_counts.tab" ftype="tabular"/>
96 <output name="fraction_counts" file="Samp-paired_fraction_counts.tab" ftype="tabular"/> 110 <output name="fraction_counts" file="Samp-paired_fraction_counts.tab" ftype="tabular"/>
97 </test> 111 </test>
112 <test>
113 <param name="seq_method_list" value="single-read"/>
114 <param name="input_fastq" value="Samp.fastq.gz" ftype="fastq.gz"/>
115 <param name="genome" value="chrM.fa" ftype="fasta"/>
116 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/>
117 <output name="bowtie_alignments" file="aligned_reads.tab" ftype="tabular"/>
118 <output name="class_fraction_counts" file="Samp_class_fraction_counts.tabular" ftype="tabular"/>
119 <output name="family_fraction_counts" file="Samp_family_fraction_counts.tabular" ftype="tabular"/>
120 <output name="fraction_counts" file="Samp_fraction_counts.tabular" ftype="tabular"/>
121 </test>
122 <test>
123 <param name="seq_method_list" value="paired-end"/>
124 <param name="input_fastq" value="Samp_L.fastq.gz" ftype="fastq.gz"/>
125 <param name="input2_fastq" value="Samp_R.fastq.gz" ftype="fastq.gz"/>
126 <param name="genome" value="chrM.fa" ftype="fasta"/>
127 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/>
128 <output name="bowtie_alignments" file="paired-aligned_reads.tab" ftype="tabular"/>
129 <output name="class_fraction_counts" file="Samp-paired_class_fraction_counts.tab" ftype="tabular"/>
130 <output name="family_fraction_counts" file="Samp-paired_family_fraction_counts.tab" ftype="tabular"/>
131 <output name="fraction_counts" file="Samp-paired_fraction_counts.tab" ftype="tabular"/>
132 </test>
98 </tests> 133 </tests>
99 134
100 <help> 135 <help>
101 136
102 **What it does** 137 **What it does**