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comparison findcluster.xml @ 12:c7ee722e48ad draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
author mvdbeek
date Tue, 14 Mar 2017 07:11:13 -0400
parents ddd06bee6a92
children 0bc66a93a62e
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11:ddd06bee6a92 12:c7ee722e48ad
1 <tool id="findcluster" name="Find clusters of reads" version="0.3.6"> 1 <tool id="findcluster" name="Find clusters of reads" version="0.3.7">
2 <description>in bam files</description> 2 <description>in bam files</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.3.6">readtagger</requirement> 4 <requirement type="package" version="0.3.7">readtagger</requirement>
5 </requirements> 5 </requirements>
6 <version_command>findcluster --version</version_command> 6 <version_command>findcluster --version</version_command>
7 <command detect_errors="aggressive"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
8 findcluster 8 findcluster
9 --input_path '$input' 9 --input_path '$input'
10 #if $reference_fasta:
11 --reference_fasta '$reference_fasta'
12 #end if
10 --output_bam '$output_bam' 13 --output_bam '$output_bam'
11 --output_gff '$output_gff' 14 --output_gff '$output_gff'
12 --sample_name '$input.element_identifier' 15 --sample_name '$input.element_identifier'
13 --threads "\${GALAXY_SLOTS:-2}" 16 --threads "\${GALAXY_SLOTS:-2}"
14 ]]></command> 17 ]]></command>
15 <inputs> 18 <inputs>
16 <param name="input" argument="--input_path" type="data" format="bam"/> 19 <param name="input" argument="--input_path" type="data" format="bam"/>
20 <param argument="--reference_fasta" label="Reference Fasta" help="Reconstructed contigs at clusters will be blasted against this sequence." type="data" format="fasta" optional="True"/>
17 </inputs> 21 </inputs>
18 <outputs> 22 <outputs>
19 <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/> 23 <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/>
20 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/> 24 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/>
21 </outputs> 25 </outputs>
23 <test> 27 <test>
24 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> 28 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
25 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/> 29 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
26 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0"/> 30 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0"/>
27 </test> 31 </test>
32 <test>
33 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
34 <param name="reference_fasta" value="reference.fasta" ftype="fasta"/>
35 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
36 <output name="output_gff">
37 <assert_contents>
38 <has_text text="FBti0019066_rover_Gypsy" />
39 </assert_contents>
40 </output>
41 </test>
28 </tests> 42 </tests>
29 <help><![CDATA[ 43 <help><![CDATA[
30 .. code-block:: 44 .. code-block::
31 45
32 Find clusters of reads that support a TE insertion. 46 Usage: findcluster [OPTIONS]
33 47
34 optional arguments: 48 Find clusters of reads that support a TE insertion.
35 -h, --help show this help message and exit 49
36 --input_path INPUT_PATH 50 Options:
37 Find cluster in this BAM file. (default: None) 51 --input_path PATH Find cluster in this BAM file.
38 --output_bam OUTPUT_BAM 52 --output_bam PATH Write out BAM file with cluster information
39 Write out BAM file with cluster information to this 53 to this path. Reads will have an additional
40 path. Reads will have an additional "CD" tag to 54 "CD" tag to indicate the cluster number
41 indicate the cluster number (default: None) 55 --output_gff PATH Write out GFF file with cluster information
42 --output_gff OUTPUT_GFF 56 to this path.
43 Write out GFF file with cluster information to this 57 --sample_name TEXT Sample name to use when writing out clusters
44 path. (default: None) 58 in GFF file. Default is to infer the name
45 --version show program's version number and exit 59 from the input filename.
60 --include_duplicates / --no-include_duplicates
61 Include reads marked as duplicates when
62 finding clusters.
63 --reference_fasta TEXT Blast cluster contigs against this fasta
64 file
65 --blastdb TEXT Blast cluster contigs against this blast
66 database
67 --threads INTEGER RANGE Threads to use for cap3 assembly step
68 --version Show the version and exit.
69 --help Show this message and exit.
70
46 71
47 ]]></help> 72 ]]></help>
48 </tool> 73 </tool>