Mercurial > repos > drosofff > repenrich
diff repenrich.xml @ 1:54a3f3a195d6 draft
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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--- a/repenrich.xml Tue May 23 18:37:22 2017 -0400 +++ b/repenrich.xml Mon May 29 13:11:57 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="repenrich" name="RepEnrich" version="0.2.0"> +<tool id="repenrich" name="RepEnrich" version="0.3.0"> <description>Repeat Element Profiling</description> <requirements> <requirement type="package" version="1.2.0">bowtie</requirement> @@ -18,7 +18,10 @@ ln -f -s '$input_fastq' '${input_base}.fastq' && bowtie-build '$genome' ${baseReference} && python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} && - bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam && + 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 && + ALIGNED=\$(grep 'reads with at least one' bowtie_alignments.txt | cut -d ' ' -f 9) && + NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && + echo \$((\$ALIGNED-\$NONALIGNED)) > bowtie_aligned.numb && samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam && samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted && mv ${input_base}_unique_sorted.bam ${input_base}_unique.bam && @@ -38,6 +41,8 @@ </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"> @@ -51,6 +56,7 @@ <param name="input_fastq" value="Samp.fastq" ftype="fastq"/> <param name="genome" value="chrM.fa" ftype="fasta"/> <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/> + <output name="bowtie_alignments" file="aligned_reads.tab" ftype="tabular"/> <output name="class_fraction_counts" file="Samp_class_fraction_counts.tabular" ftype="tabular"/> <output name="family_fraction_counts" file="Samp_family_fraction_counts.tabular" ftype="tabular"/> <output name="fraction_counts" file="Samp_fraction_counts.tabular" ftype="tabular"/>