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comparison inner_distance.xml @ 32:580ee0c4bc4e

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Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
author lparsons
date Mon, 07 Oct 2013 15:01:13 -0400
parents cc5eaa9376d8
children
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31:cc5eaa9376d8 32:580ee0c4bc4e
1 <tool id="inner_distance" name="Inner Distance" version="1.1"> 1 <tool id="rseqc_inner_distance" name="Inner Distance" version="1.1">
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 <requirements> 3 <requirements>
4 <requirement type="package" version="2.11.0">R</requirement> 4 <requirement type="package" version="3.0.1">R</requirement>
5 <requirement type="package" version="1.7.1">numpy</requirement> 5 <requirement type="package" version="1.7.1">numpy</requirement>
6 <requirement type="package" version="2.3.7">rseqc</requirement> 6 <requirement type="package" version="2.3.7">rseqc</requirement>
7 </requirements> 7 </requirements>
8 <command> inner_distance.py -i $input -o output -r $refgene 8 <command>
9 inner_distance.py -i $input -o output -r $refgene
9 10
10 #if $bounds.hasLowerBound 11 #if $bounds.hasLowerBound
11 -l $bounds.lowerBound 12 -l $bounds.lowerBound
12 #end if 13 #end if
13 14
14 #if $bounds2.hasUpperBound 15 #if $bounds2.hasUpperBound
15 -u $bounds2.upperBound 16 -u $bounds2.upperBound
16 #end if 17 #end if
17 18
18 #if $steps.step 19 #if $steps.step
19 -s $steps.stepSize 20 -s $steps.stepSize
20 #end if 21 #end if
21 </command> 22 </command>
22 <inputs>
23 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
24 <param name="refgene" type="data" format="bed" label="reference gene model" />
25 <conditional name="bounds">
26 <param name="hasLowerBound" type="boolean" label="Specify lower bound" value="false"/>
27 <when value="true">
28 <param name="lowerBound" type="integer" value="-250" label="Estimated Lower Bound (bp, default=-250)" />
29 </when>
30 </conditional>
31 <conditional name="bounds2">
32 <param name="hasUpperBound" type="boolean" label="Specify upper bound" value="false" />
33 <when value="true">
34 <param name="upperBound" type="integer" value="250" label="Estimated Upper Bound (bp, default=250)" />
35 </when>
36 </conditional>
37 <conditional name="steps">
38 <param name="step" type="boolean" label="Specify step size" value="false" />
39 <when value="true">
40 <param name="stepSize" type="integer" value="5" label="Step size (bp, default=5)" />
41 </when>
42 </conditional>
43 </inputs>
44 <outputs>
45 <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string} (Text)"/>
46 <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string} (Freq Text)" />
47 <data format="pdf" name="outputpdf" from_work_dir="output.inner_distance_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
48 <data format="r" name="outputr" from_work_dir="output.inner_distance_plot.r" label="${tool.name} on ${on_string} (R Script)" />
49 </outputs>
50 <stdio> 23 <stdio>
51 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> 24 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
52 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> 25 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
53 </stdio> 26 </stdio>
54 <help> 27 <inputs>
28 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
29 <param name="refgene" type="data" format="bed" label="reference gene model" />
30 <conditional name="bounds">
31 <param name="hasLowerBound" type="boolean" label="Specify lower bound" value="false"/>
32 <when value="true">
33 <param name="lowerBound" type="integer" value="-250" label="Estimated Lower Bound (bp, default=-250)" />
34 </when>
35 </conditional>
36 <conditional name="bounds2">
37 <param name="hasUpperBound" type="boolean" label="Specify upper bound" value="false" />
38 <when value="true">
39 <param name="upperBound" type="integer" value="250" label="Estimated Upper Bound (bp, default=250)" />
40 </when>
41 </conditional>
42 <conditional name="steps">
43 <param name="step" type="boolean" label="Specify step size" value="false" />
44 <when value="true">
45 <param name="stepSize" type="integer" value="5" label="Step size (bp, default=5)" />
46 </when>
47 </conditional>
48 </inputs>
49 <outputs>
50 <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string} (Text)"/>
51 <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string} (Freq Text)" />
52 <data format="pdf" name="outputpdf" from_work_dir="output.inner_distance_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
53 <data format="txt" name="outputr" from_work_dir="output.inner_distance_plot.r" label="${tool.name} on ${on_string} (R Script)" />
54 </outputs>
55 <help>
55 inner_distance.py 56 inner_distance.py
56 +++++++++++++++++ 57 +++++++++++++++++
57 58
58 This module is used to calculate the inner distance (or insert size) between two paired RNA 59 This module is used to calculate the inner distance (or insert size) between two paired RNA
59 reads. The distance is the mRNA length between two paired fragments. We first determine the 60 reads. The distance is the mRNA length between two paired fragments. We first determine the
69 70
70 Inputs 71 Inputs
71 ++++++++++++++ 72 ++++++++++++++
72 73
73 Input BAM/SAM file 74 Input BAM/SAM file
74 Alignment file in BAM/SAM format. 75 Alignment file in BAM/SAM format.
75 76
76 Reference gene model 77 Reference gene model
77 Gene model in BED format. 78 Gene model in BED format.
78 79
79 Estimated Upper/Lower Bounds (defaults=250 and -250) 80 Estimated Upper/Lower Bounds (defaults=250 and -250)
80 Estimated upper/lower bounds of inner distance (bp). 81 Estimated upper/lower bounds of inner distance (bp).
81 82
82 Step size (default=5) 83 Step size (default=5)
83 Step size of histogram 84 Step size of histogram
84 85
85 86
86 Output 87 Output
87 ++++++++++++++ 88 ++++++++++++++
88 89
116 .. image:: http://rseqc.sourceforge.net/_static/logo.png 117 .. image:: http://rseqc.sourceforge.net/_static/logo.png
117 118
118 .. _RSeQC: http://rseqc.sourceforge.net/ 119 .. _RSeQC: http://rseqc.sourceforge.net/
119 120
120 121
121 </help> 122 </help>
122 </tool> 123 </tool>