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comparison repenrich.xml @ 2:15e3e29f310e draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
author artbio
date Tue, 19 Sep 2017 17:23:15 -0400
parents 51b4590a972d
children 1c9810ba0638
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1:51b4590a972d 2:15e3e29f310e
1 <tool id="repenrich" name="RepEnrich" version="1.4.1"> 1 <tool id="repenrich" name="RepEnrich" version="1.4.2">
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>
22 python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} && 22 python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} &&
23 #if $seq_method.seq_method_list == "single-read": 23 #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 && 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 &&
25 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) && 25 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) &&
26 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && 26 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) &&
27 echo \$((\$TOTAL-\$NONALIGNED)) > bowtie_aligned.numb && 27 echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb &&
28 echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb &&
28 #else: 29 #else:
29 bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq -1 ${input_base}.fastq -2 ${input_base}_2.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt && 30 bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq -1 ${input_base}.fastq -2 ${input_base}_2.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt &&
30 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) && 31 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) &&
31 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && 32 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) &&
32 echo \$((\$TOTAL-\$NONALIGNED)) > bowtie_aligned.numb && 33 echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb &&
34 echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb &&
33 #end if 35 #end if
34 samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam && 36 samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam &&
35 samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted && 37 samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted &&
36 mv ${input_base}_unique_sorted.bam ${input_base}_unique.bam && 38 mv ${input_base}_unique_sorted.bam ${input_base}_unique.bam &&
37 samtools index ${input_base}_unique.bam && 39 samtools index ${input_base}_unique.bam &&
63 <param format="fasta" label="Reference genome in fasta format" name="genome" type="data" /> 65 <param format="fasta" label="Reference genome in fasta format" name="genome" type="data" />
64 <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/> 66 <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/>
65 </inputs> 67 </inputs>
66 68
67 <outputs> 69 <outputs>
68 <data format="tabular" name="bowtie_alignments" label="RepEnrich on ${on_string}: reads aligned" from_work_dir="bowtie_aligned.numb"> 70 <data format="tabular" name="bowtie_alignments" label="RepEnrich on ${on_string}: reads aligned" from_work_dir="bowtie_aligned.numb" />
69 </data> 71 <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tabular" />
70 <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tabular"> 72 <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tabular" />
71 </data> 73 <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tabular" />
72 <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tabular">
73 </data>
74 <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tabular">
75 </data>
76 </outputs> 74 </outputs>
77 75
78 <tests> 76 <tests>
79 <test> 77 <test>
80 <param name="seq_method_list" value="single-read"/> 78 <param name="seq_method_list" value="single-read"/>