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comparison inner_distance.xml @ 51:09846d5169fa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
author iuc
date Tue, 14 Mar 2017 10:23:21 -0400
parents 6b33e31bda10
children 5873cd7afb67
comparison
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50:f242ee103277 51:09846d5169fa
1 <tool id="rseqc_inner_distance" name="Inner Distance" version="2.4galaxy1"> 1 <tool id="rseqc_inner_distance" name="Inner Distance" version="@WRAPPER_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 3
4 <macros> 4 <macros>
5 <import>rseqc_macros.xml</import> 5 <import>rseqc_macros.xml</import>
6 </macros> 6 </macros>
7 7
8 <requirements> 8 <expand macro="requirements" />
9 <expand macro="requirement_package_r" />
10 <expand macro="requirement_package_numpy" />
11 <expand macro="requirement_package_rseqc" />
12 </requirements>
13 9
14 <expand macro="stdio" /> 10 <expand macro="stdio" />
15 11
16 <version_command><![CDATA[inner_distance.py --version]]></version_command> 12 <version_command><![CDATA[inner_distance.py --version]]></version_command>
17 13
18 <command><![CDATA[ 14 <command><![CDATA[
19 inner_distance.py -i $input -o output -r $refgene 15 inner_distance.py -i '${input}' -o output -r '${refgene}'
20 --sample-size $sample_size 16 --sample-size ${sample_size}
21 --lower-bound $lowerBound 17 --lower-bound ${lowerBound}
22 --upper-bound $upperBound 18 --upper-bound ${upperBound}
23 --step $step 19 --step ${step}
24 --mapq $mapq 20 --mapq ${mapq}
25 ]]> 21 ]]>
26 </command> 22 </command>
27 23
28 <inputs> 24 <inputs>
29 <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)" /> 25 <expand macro="bam_sam_param" />
30 <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)" /> 26 <expand macro="refgene_param" />
31 <param name="sample_size" type="integer" label="Number of read-pairs used to estimate inner distance (default = 1000000)" value="1000000" help="(--sample-size)"/> 27 <expand macro="sample_size_param" />
32 <param name="lowerBound" type="integer" value="-250" label="Lower bound (bp, default=-250)" help="Used for plotting histogram (--lower-bound)"/> 28 <param name="lowerBound" type="integer" value="-250" label="Lower bound (bp, default=-250)" help="Used for plotting histogram (--lower-bound)"/>
33 <param name="upperBound" type="integer" value="250" label="Upper bound (bp, default=250)" help="Used for plotting histogram (--upper-bound)"/> 29 <param name="upperBound" type="integer" value="250" label="Upper bound (bp, default=250)" help="Used for plotting histogram (--upper-bound)"/>
34 <param name="step" type="integer" value="5" label="Step size of histogram (bp, default=5)" help="(--step)"/> 30 <param name="step" type="integer" value="5" label="Step size of histogram (bp, default=5)" help="(--step)"/>
35 <param name="mapq" type="integer" label="Minimum mapping quality (default=30)" help="Minimum phred scale mapping quality to consider a read 'uniquely mapped' (--mapq)" value="30" /> 31 <expand macro="mapq_param" />
32 <expand macro="rscript_output_param" />
36 </inputs> 33 </inputs>
37 34
38 <outputs> 35 <outputs>
39 <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string} (Text)"/> 36 <expand macro="pdf_output_data" filename="output.inner_distance_plot.pdf" />
40 <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string} (Freq Text)" /> 37 <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string} (text)"/>
41 <data format="pdf" name="outputpdf" from_work_dir="output.inner_distance_plot.pdf" label="${tool.name} on ${on_string} (PDF)" /> 38 <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string} (frequency text)" />
42 <data format="txt" name="outputr" from_work_dir="output.inner_distance_plot.r" label="${tool.name} on ${on_string} (R Script)" /> 39 <expand macro="rscript_output_data" filename="output.inner_distance_plot.r" />
43 </outputs> 40 </outputs>
44 41
45 <tests> 42 <tests>
46 <test> 43 <test>
47 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 44 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
48 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/> 45 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
49 <output name="outputtxt" file="output.inner_distance.txt"/> 46 <param name="rscript_output" value="true" />
50 <output name="outputfreqtxt" file="output.inner_distance_freq.txt"/> 47 <output name="outputtxt" file="output.inner_distance.txt" />
51 <output name="outputpdf" file="output.inner_distance_plot.pdf"/> 48 <output name="outputfreqtxt" file="output.inner_distance_freq.txt" />
52 <output name="outputr" file="output.inner_distance_plot.r"/> 49 <output name="outputpdf" file="output.inner_distance_plot.pdf" compare="sim_size"/>
50 <output name="outputr" file="output.inner_distance_plot.r" />
53 </test> 51 </test>
54 </tests> 52 </tests>
55 53
56 <help><![CDATA[ 54 <help><![CDATA[
57 inner_distance.py 55 inner_distance.py
98 - number of read pairs 96 - number of read pairs
99 - note the first 2 columns are left side half open interval 97 - note the first 2 columns are left side half open interval
100 3. output.inner_distance_plot.r: R script to generate histogram 98 3. output.inner_distance_plot.r: R script to generate histogram
101 4. output.inner_distance_plot.pdf: histogram plot 99 4. output.inner_distance_plot.pdf: histogram plot
102 100
103 .. image:: http://rseqc.sourceforge.net/_images/inner_distance.png 101 .. image:: $PATH_TO_IMAGES/inner_distance.png
104 :height: 600 px 102 :height: 600 px
105 :width: 600 px 103 :width: 600 px
106 :scale: 80 % 104 :scale: 80 %
107 105
108 106 @ABOUT@
109 -----
110
111 About RSeQC
112 +++++++++++
113
114 The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.
115
116 The RSeQC package is licensed under the GNU GPL v3 license.
117
118 .. image:: http://rseqc.sourceforge.net/_static/logo.png
119
120 .. _RSeQC: http://rseqc.sourceforge.net/
121 107
122 ]]> 108 ]]>
123 </help> 109 </help>
124 110
125 <expand macro="citations" /> 111 <expand macro="citations" />