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comparison inner_distance.xml @ 63:27e16a30667a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 5968573462fa
children
comparison
equal deleted inserted replaced
62:473382134e56 63:27e16a30667a
1 <tool id="rseqc_inner_distance" name="Inner Distance" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> 1 <tool id="rseqc_inner_distance" name="Inner Distance" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
2 <description>calculate the inner distance (or insert size) between two paired RNA reads</description> 2 <description>calculate the inner distance (or insert size) between two paired RNA reads</description>
3 <macros> 3 <macros>
4 <import>rseqc_macros.xml</import> 4 <import>rseqc_macros.xml</import>
5 </macros> 5 </macros>
6
7 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
8 7 <expand macro="requirements"/>
9 <expand macro="requirements" /> 8 <expand macro="stdio"/>
10
11 <expand macro="stdio" />
12
13 <version_command><![CDATA[inner_distance.py --version]]></version_command> 9 <version_command><![CDATA[inner_distance.py --version]]></version_command>
14
15 <command><![CDATA[ 10 <command><![CDATA[
16 @BAM_SAM_INPUTS@ 11 @BAM_SAM_INPUTS@
17 inner_distance.py -i 'input.${extension}' -o output -r '${refgene}' 12 inner_distance.py -i 'input.${extension}' -o output -r '${refgene}'
18 --sample-size ${sample_size} 13 --sample-size ${sample_size}
19 --lower-bound ${lowerBound} 14 --lower-bound ${lowerBound}
20 --upper-bound ${upperBound} 15 --upper-bound ${upperBound}
21 --step ${step} 16 --step ${step}
22 --mapq ${mapq} 17 --mapq ${mapq}
23 ]]> 18 ]]>
24 </command> 19 </command>
25
26 <inputs> 20 <inputs>
27 <expand macro="bam_sam_param" /> 21 <expand macro="bam_sam_param"/>
28 <expand macro="refgene_param" /> 22 <expand macro="refgene_param"/>
29 <expand macro="sample_size_param" /> 23 <expand macro="sample_size_param"/>
30 <param name="lowerBound" type="integer" value="-250" label="Lower bound (bp, default=-250)" help="Used for plotting histogram (--lower-bound)"/> 24 <param name="lowerBound" type="integer" value="-250" label="Lower bound (bp, default=-250)" help="Used for plotting histogram (--lower-bound)"/>
31 <param name="upperBound" type="integer" value="250" label="Upper bound (bp, default=250)" help="Used for plotting histogram (--upper-bound)"/> 25 <param name="upperBound" type="integer" value="250" label="Upper bound (bp, default=250)" help="Used for plotting histogram (--upper-bound)"/>
32 <param name="step" type="integer" value="5" label="Step size of histogram (bp, default=5)" help="(--step)"/> 26 <param name="step" type="integer" value="5" label="Step size of histogram (bp, default=5)" help="(--step)"/>
33 <expand macro="mapq_param" /> 27 <expand macro="mapq_param"/>
34 <expand macro="rscript_output_param" /> 28 <expand macro="rscript_output_param"/>
35 </inputs> 29 </inputs>
36
37 <outputs> 30 <outputs>
38 <expand macro="pdf_output_data" filename="output.inner_distance_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/> 31 <expand macro="pdf_output_data" filename="output.inner_distance_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/>
39 <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string}: TXT"/> 32 <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string}: TXT"/>
40 <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string}: frequency (TXT)" /> 33 <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string}: frequency (TXT)"/>
41 <expand macro="rscript_output_data" filename="output.inner_distance_plot.r" label="${tool.name} on ${on_string}: Rscript"/> 34 <expand macro="rscript_output_data" filename="output.inner_distance_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
42 </outputs> 35 </outputs>
43
44 <tests> 36 <tests>
45 <test> 37 <test expect_num_outputs="4">
46 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 38 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
47 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> 39 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
48 <param name="rscript_output" value="true" /> 40 <param name="rscript_output" value="true"/>
49 <output name="outputtxt" file="output.inner_distance.txt" /> 41 <output name="outputtxt" file="output.inner_distance.txt"/>
50 <output name="outputfreqtxt" file="output.inner_distance_freq.txt" /> 42 <output name="outputfreqtxt" file="output.inner_distance_freq.txt"/>
51 <output name="outputpdf" file="output.inner_distance_plot.pdf" compare="sim_size"/> 43 <output name="outputpdf" file="output.inner_distance_plot.pdf" compare="sim_size"/>
52 <output name="outputr" file="output.inner_distance_plot_r" /> 44 <output name="outputr" file="output.inner_distance_plot_r"/>
53 </test> 45 </test>
54 </tests> 46 </tests>
55
56 <help><![CDATA[ 47 <help><![CDATA[
57 inner_distance.py 48 inner_distance.py
58 +++++++++++++++++ 49 +++++++++++++++++
59 50
60 This module is used to calculate the inner distance (or insert size) between two paired RNA 51 This module is used to calculate the inner distance (or insert size) between two paired RNA
107 98
108 @ABOUT@ 99 @ABOUT@
109 100
110 ]]> 101 ]]>
111 </help> 102 </help>
112 103 <expand macro="citations"/>
113 <expand macro="citations" />
114
115 </tool> 104 </tool>