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comparison repenrich.xml @ 1:54a3f3a195d6 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
author drosofff
date Mon, 29 May 2017 13:11:57 -0400
parents 1435d142041b
children aed130b47d36
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0:1435d142041b 1:54a3f3a195d6
1 <tool id="repenrich" name="RepEnrich" version="0.2.0"> 1 <tool id="repenrich" name="RepEnrich" version="0.3.0">
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>
16 #set baseReference = re.sub('.fa$', '', $baseReference) 16 #set baseReference = re.sub('.fa$', '', $baseReference)
17 ln -f -s '$genome' '${baseReference}.fa' && 17 ln -f -s '$genome' '${baseReference}.fa' &&
18 ln -f -s '$input_fastq' '${input_base}.fastq' && 18 ln -f -s '$input_fastq' '${input_base}.fastq' &&
19 bowtie-build '$genome' ${baseReference} && 19 bowtie-build '$genome' ${baseReference} &&
20 python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} && 20 python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} &&
21 bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam && 21 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 &&
22 ALIGNED=\$(grep 'reads with at least one' bowtie_alignments.txt | cut -d ' ' -f 9) &&
23 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) &&
24 echo \$((\$ALIGNED-\$NONALIGNED)) > bowtie_aligned.numb &&
22 samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam && 25 samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam &&
23 samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted && 26 samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted &&
24 mv ${input_base}_unique_sorted.bam ${input_base}_unique.bam && 27 mv ${input_base}_unique_sorted.bam ${input_base}_unique.bam &&
25 samtools index ${input_base}_unique.bam && 28 samtools index ${input_base}_unique.bam &&
26 rm ${input_base}_unique.sam && 29 rm ${input_base}_unique.sam &&
36 <param format="fastq,fastqsanger" label="Single-reads equencing dataset" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> 39 <param format="fastq,fastqsanger" label="Single-reads equencing dataset" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" />
37 <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/> 40 <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/>
38 </inputs> 41 </inputs>
39 42
40 <outputs> 43 <outputs>
44 <data format="tabular" name="bowtie_alignments" label="RepEnrich on ${on_string}: reads aligned" from_work_dir="bowtie_aligned.numb">
45 </data>
41 <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tabular"> 46 <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tabular">
42 </data> 47 </data>
43 <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tabular"> 48 <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tabular">
44 </data> 49 </data>
45 <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tabular"> 50 <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tabular">
49 <tests> 54 <tests>
50 <test> 55 <test>
51 <param name="input_fastq" value="Samp.fastq" ftype="fastq"/> 56 <param name="input_fastq" value="Samp.fastq" ftype="fastq"/>
52 <param name="genome" value="chrM.fa" ftype="fasta"/> 57 <param name="genome" value="chrM.fa" ftype="fasta"/>
53 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/> 58 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/>
59 <output name="bowtie_alignments" file="aligned_reads.tab" ftype="tabular"/>
54 <output name="class_fraction_counts" file="Samp_class_fraction_counts.tabular" ftype="tabular"/> 60 <output name="class_fraction_counts" file="Samp_class_fraction_counts.tabular" ftype="tabular"/>
55 <output name="family_fraction_counts" file="Samp_family_fraction_counts.tabular" ftype="tabular"/> 61 <output name="family_fraction_counts" file="Samp_family_fraction_counts.tabular" ftype="tabular"/>
56 <output name="fraction_counts" file="Samp_fraction_counts.tabular" ftype="tabular"/> 62 <output name="fraction_counts" file="Samp_fraction_counts.tabular" ftype="tabular"/>
57 </test> 63 </test>
58 </tests> 64 </tests>