Mercurial > repos > artbio > sr_bowtie_dataset_annotation
diff sr_bowtie_dataset_annotation.xml @ 9:6bf9de09aa74 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
author | artbio |
---|---|
date | Mon, 11 Apr 2022 00:27:41 +0000 |
parents | 3519c2de7fac |
children | fd4a60fc3fca |
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--- a/sr_bowtie_dataset_annotation.xml Sat Apr 09 22:45:21 2022 +0000 +++ b/sr_bowtie_dataset_annotation.xml Mon Apr 11 00:27:41 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.6"> +<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.7"> <description>by iterative alignments with sRbowtie</description> <requirements> <requirement type="package" version="1.3.1">bowtie</requirement> @@ -24,7 +24,9 @@ #elif $input[0].is_of_type('fastq'): #set format = "-q" #end if - + + mkdir unmatched_dir && + #for $file in $input: #set sample=$file.element_identifier bowtie -p \${GALAXY_SLOTS:-4} @@ -58,12 +60,15 @@ #end for remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) && echo -e "$sample\tNot classified\t\${remaining}\t\${genome_aligned}" >> $output && + cp class_unmatched.fa unmatched_dir/${sample}_unmatched.fasta && + #if $format == '-q': + mv unmatched_dir/${sample}_unmatched.fasta unmatched_dir/${sample}_unmatched.fastq && + sed -n '1~4s/^@/>/p;2~4p' unmatched_dir/${sample}_unmatched.fastq > unmatched_dir/${sample}_unmatched.fasta && + rm unmatched_dir/${sample}_unmatched.fastq && + #end if #end for + ls -la unmatched_dir && Rscript $__tool_directory__/barplot.r --input $output --barplot $barplot - #if $format == '-q': - && mv class_unmatched.fa class_unmatched.fastq - && sed -n '1~4s/^@/>/p;2~4p' class_unmatched.fastq > class_unmatched.fa - #end if ]]></command> <inputs> <param name="input" type="data" multiple="True" format="fasta,fastq" label="Input file: reads clipped from their adapter" help="Only with clipped, raw fasta or fastq files"/> @@ -96,7 +101,9 @@ <!-- End of other bowtie index selections --> </inputs> <outputs> - <data format="fasta" name="unmatched" label="Annotate smRNAs: Unmatched reads" from_work_dir="class_unmatched.fa" /> + <collection name="unmatched" type="list" format="fasta" label="Annotate smRNAs: Unmatched reads"> + <discover_datasets pattern="__name_and_ext__" directory="unmatched_dir" /> + </collection> <data format="tabular" name="output" label="Cascade Annotation Analysis"> <actions> <action name="column_names" type="metadata" default="Sample,Reference Index,Number of reads, Total reads" /> @@ -106,6 +113,22 @@ </outputs> <tests> <test> + <param name="input" value ="sample5.fa,sample4.fa,sample3.fa,sample2.fa,sample1.fa" ftype="fasta" /> + <param name="genomeSource" value="history" /> + <param name="ownFile" value ="2L-tail.fa" ftype="fasta" /> + <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" /> + <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" /> + <output name="output" ftype="tabular" file="multisample5_output.tab" /> + <output name="barplot" ftype="pdf" file="multisample5_output.pdf" compare="sim_size" delta="500" /> + <output_collection name="unmatched" type="list" count="5"> + <element name="sample5.fa_unmatched" file="unmatched_5.fa" ftype="fasta"/> + <element name="sample4.fa_unmatched" file="unmatched_4.fa" ftype="fasta"/> + <element name="sample3.fa_unmatched" file="unmatched_3.fa" ftype="fasta"/> + <element name="sample2.fa_unmatched" file="unmatched_2.fa" ftype="fasta"/> + <element name="sample1.fa_unmatched" file="unmatched_1.fa" ftype="fasta"/> + </output_collection> + </test> + <test> <param name="input" value ="sample1.fa" ftype="fasta" /> <param name="genomeSource" value="history" /> <param name="ownFile" value ="2L-tail.fa" ftype="fasta" /> @@ -113,7 +136,9 @@ <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" /> <output name="output" ftype="tabular" file="sample1_output.tab" /> <output name="barplot" ftype="pdf" file="sample1_output.pdf" compare="sim_size" delta="500"/> - <output name="unmatched" ftype="fasta" file="unmatched_1.fa" /> + <output_collection name="unmatched" type="list"> + <element name="sample1.fa_unmatched" file="unmatched_1.fa" ftype="fasta"/> + </output_collection> </test> <test> <param name="input" value ="sample.fastq" ftype="fastq" /> @@ -123,17 +148,9 @@ <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" /> <output name="output" ftype="tabular" file="sample_output.tab" /> <output name="barplot" ftype="pdf" file="sample_output.pdf" compare="sim_size" delta="500"/> - <output name="unmatched" ftype="fasta" file="unmatched_2.fa" /> - </test> - <test> - <param name="input" value ="sample5.fa,sample4.fa,sample3.fa,sample2.fa,sample1.fa" ftype="fasta" /> - <param name="genomeSource" value="history" /> - <param name="ownFile" value ="2L-tail.fa" ftype="fasta" /> - <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" /> - <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" /> - <output name="output" ftype="tabular" file="multisample5_output.tab" /> - <output name="barplot" ftype="pdf" file="multisample5_output.pdf" compare="sim_size" delta="500" /> - <output name="unmatched" ftype="fasta" file="unmatched_3.fa" /> + <output_collection name="unmatched" type="list"> + <element name="sample.fastq_unmatched" file="unmatched_fastq.fa" ftype="fasta"/> + </output_collection> </test> </tests> <help>