Mercurial > repos > artbio > repenrich
diff repenrich.xml @ 2:15e3e29f310e draft
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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--- a/repenrich.xml Mon Sep 18 17:22:07 2017 -0400 +++ b/repenrich.xml Tue Sep 19 17:23:15 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="repenrich" name="RepEnrich" version="1.4.1"> +<tool id="repenrich" name="RepEnrich" version="1.4.2"> <description>Repeat Element Profiling</description> <requirements> <requirement type="package" version="1.2.0">bowtie</requirement> @@ -24,12 +24,14 @@ 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 && TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) && NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && - echo \$((\$TOTAL-\$NONALIGNED)) > bowtie_aligned.numb && + echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb && + echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb && #else: 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 && TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) && NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && - echo \$((\$TOTAL-\$NONALIGNED)) > bowtie_aligned.numb && + echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb && + echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb && #end if samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam && samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted && @@ -65,14 +67,10 @@ </inputs> <outputs> - <data format="tabular" name="bowtie_alignments" label="RepEnrich on ${on_string}: reads aligned" from_work_dir="bowtie_aligned.numb"> - </data> - <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tabular"> - </data> - <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tabular"> - </data> - <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tabular"> - </data> + <data format="tabular" name="bowtie_alignments" label="RepEnrich on ${on_string}: reads aligned" from_work_dir="bowtie_aligned.numb" /> + <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tabular" /> + <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tabular" /> + <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tabular" /> </outputs> <tests>