Mercurial > repos > mvdbeek > bam_readtagger
diff findcluster.xml @ 31:301316cb596a draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
author | mvdbeek |
---|---|
date | Wed, 21 Jun 2017 09:38:25 -0400 |
parents | db5c766503dd |
children | bf3d04937095 |
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--- a/findcluster.xml Thu May 11 05:33:27 2017 -0400 +++ b/findcluster.xml Wed Jun 21 09:38:25 2017 -0400 @@ -1,7 +1,10 @@ -<tool id="findcluster" name="Find clusters of reads" version="0.3.24"> +<tool id="findcluster" name="Find clusters of reads" version="0.3.25"> <description>in bam files</description> + <macros> + <import>macros.xml</import> + </macros> <requirements> - <requirement type="package" version="0.3.24">readtagger</requirement> + <requirement type="package" version="0.3.25">readtagger</requirement> </requirements> <version_command>findcluster --version</version_command> <command detect_errors="aggressive"><![CDATA[ @@ -9,8 +12,19 @@ ln -f -s $input.metadata.bam_index input.bam.bai && findcluster --input_path input.bam - #if $reference_fasta: - --reference_fasta '$reference_fasta' + #if $transposon_source.ref_file: + #if str($transposon_source.reference_source_selector) == "history": + --transposon_reference_fasta '$transposon_source.ref_file' + #else : + --transposon_bwa_index '$reference_source.ref_file.fields.path' + #end if + #end if + #if $genome_source.ref_file: + #if str($genome_source.reference_source_selector) == "history": + --genome_reference_fasta '$genome_source.ref_file' + #else : + --genome_bwa_index '$reference_source.ref_file.fields.path' + #end if #end if --output_bam '$output_bam' --output_gff '$output_gff' @@ -20,7 +34,9 @@ ]]></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"/> + + <expand macro="reference_source_conditional" reference_type="transposon"/> + <expand macro="reference_source_conditional" reference_type="genome"/> </inputs> <outputs> <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/> @@ -35,7 +51,8 @@ </test> <test> <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> - <param name="reference_fasta" value="reference.fasta" ftype="fasta"/> + <param name="transposon_source|reference_source_selector" value="history"/> + <param name="transposon_source|ref_file" 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> @@ -51,24 +68,35 @@ Find clusters of reads that support a TE insertion. - Options: + Options: --input_path PATH Find cluster in this BAM file. + --region TEXT Find clusters in this Region (Format is + chrX:2000-1000). + --max_proper_pair_size INTEGER Maximum proper pairs size. If not given will + be inferred from the data. --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. + --output_fasta PATH Write out supporting evidence for clusters + 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 + --transposon_reference_fasta TEXT + Transposon fasta to align clipped reads to. + Not necessary if BWA index is provided. + --transposon_bwa_index TEXT Transposon BWA index to align clipped reads + to + --genome_reference_fasta TEXT Genome fasta to align clipped reads to. Not + necessary if BWA index is provided. + --genome_bwa_index TEXT Genome BWA index to align clipped reads to --threads INTEGER RANGE Threads to use for cap3 assembly step + --shm_dir PATH Path to shared memory folder --version Show the version and exit. --help Show this message and exit.