Mercurial > repos > mvdbeek > bam_readtagger
diff findcluster.xml @ 11:124f7f8ee080 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
author | mvdbeek |
---|---|
date | Tue, 14 Mar 2017 07:11:26 -0400 |
parents | c179d081b6ba |
children | e64078fafd38 |
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--- a/findcluster.xml Thu Mar 09 12:25:30 2017 -0500 +++ b/findcluster.xml Tue Mar 14 07:11:26 2017 -0400 @@ -1,12 +1,15 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.3.6"> +<tool id="findcluster" name="Find clusters of reads" version="0.3.7"> <description>in bam files</description> <requirements> - <requirement type="package" version="0.3.6">readtagger</requirement> + <requirement type="package" version="0.3.7">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ findcluster --input_path '$input' + #if $reference_fasta: + --reference_fasta '$reference_fasta' + #end if --output_bam '$output_bam' --output_gff '$output_gff' --sample_name '$input.element_identifier' @@ -14,6 +17,7 @@ ]]></command> <inputs> <param name="input" argument="--input_path" type="data" format="bam"/> + <param argument="--reference_fasta" label="Reference Fasta" help="Reconstructed contigs at clusters will be blasted against this sequence." type="data" format="fasta" optional="True"/> </inputs> <outputs> <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/> @@ -25,24 +29,45 @@ <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/> <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0"/> </test> + <test> + <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> + <param name="reference_fasta" value="reference.fasta" ftype="fasta"/> + <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/> + <output name="output_gff"> + <assert_contents> + <has_text text="FBti0019066_rover_Gypsy" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ .. code-block:: - Find clusters of reads that support a TE insertion. + Usage: findcluster [OPTIONS] + + Find clusters of reads that support a TE insertion. - optional arguments: - -h, --help show this help message and exit - --input_path INPUT_PATH - Find cluster in this BAM file. (default: None) - --output_bam OUTPUT_BAM - Write out BAM file with cluster information to this - path. Reads will have an additional "CD" tag to - indicate the cluster number (default: None) - --output_gff OUTPUT_GFF - Write out GFF file with cluster information to this - path. (default: None) - --version show program's version number and exit + Options: + --input_path PATH Find cluster in this BAM file. + --output_bam PATH Write out BAM file with cluster information + to this path. Reads will have an additional + "CD" tag to indicate the cluster number + --output_gff PATH Write out GFF file with cluster information + to this path. + --sample_name TEXT Sample name to use when writing out clusters + in GFF file. Default is to infer the name + from the input filename. + --include_duplicates / --no-include_duplicates + Include reads marked as duplicates when + finding clusters. + --reference_fasta TEXT Blast cluster contigs against this fasta + file + --blastdb TEXT Blast cluster contigs against this blast + database + --threads INTEGER RANGE Threads to use for cap3 assembly step + --version Show the version and exit. + --help Show this message and exit. + ]]></help> </tool>