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comparison bedToIgv.xml @ 50:df28283b3778 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:54:22 -0400
parents 2f457890d8c8
children 7a06bb42dbb1
comparison
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49:5074e81a5ce1 50:df28283b3778
1 <tool id="bedtools_bedtoigv" name="bedtools BED to IGV" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_bedtoigv" name="bedtools BED to IGV" version="@TOOL_VERSION@">
2 <description>create batch script for taking IGV screenshots</description> 2 <description>create batch script for taking IGV screenshots</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command><![CDATA[
9 <![CDATA[ 9 bedToIgv
10 bedToIgv 10 -i '$input'
11 -i '$input' 11 #if $sort:
12 #if $sort: 12 -sort $sort
13 -sort $sort 13 #end if
14 #end if 14 $clps
15 $clps 15 $name
16 $name 16 -slop $slop
17 -slop $slop 17 -img $img
18 -img $img 18 > '$output'
19 > '$output' 19 ]]></command>
20 ]]>
21 </command>
22 <inputs> 20 <inputs>
23 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="Create IGV batch script for this @STD_BEDTOOLS_INPUT_LABEL@ file"/> 21 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Create IGV batch script for this @STD_BEDTOOLS_INPUT_LABEL@ file"/>
24 <param name="sort" type="select" label="Sort BAM file by" help="The type of BAM sorting you would like to apply to each image."> 22 <param name="sort" type="select" label="Sort BAM file by" help="The type of BAM sorting you would like to apply to each image.">
25 <option value="">No sorting at all (default)</option> 23 <option value="">No sorting at all (default)</option>
26 <option value="base">base</option> 24 <option value="base">base</option>
27 <option value="position">position</option> 25 <option value="position">position</option>
28 <option value="strand">strand</option> 26 <option value="strand">strand</option>
29 <option value="quality">quality</option> 27 <option value="quality">quality</option>
30 <option value="sample">sample</option> 28 <option value="sample">sample</option>
31 <option value="readGroup">readGroup</option> 29 <option value="readGroup">readGroup</option>
32 </param> 30 </param>
33 <param name="clps" type="boolean" truevalue="-clps" falsevalue="" label="Collapse the aligned reads prior to taking a snapshot?"/> 31 <param argument="-clps" type="boolean" truevalue="-clps" falsevalue="" label="Collapse the aligned reads prior to taking a snapshot?"/>
34 <param name="name" type="boolean" truevalue="-name" falsevalue="" label="Use the name field (column 4) for each image's filename." help="Default is to use chr:start-pos."/> 32 <param argument="-name" type="boolean" truevalue="-name" falsevalue="" label="Use the name field (column 4) for each image's filename." help="Default is to use chr:start-pos."/>
35 <param name="slop" type="integer" min="0" value="0" label="Number of flanking base pairs on the left and right of the image."/> 33 <param argument="-slop" type="integer" min="0" value="0" label="Number of flanking base pairs on the left and right of the image."/>
36 <param name="img" type="select" label="Select the type of image to be created."> 34 <param argument="-img" type="select" label="Select the type of image to be created.">
37 <option value="png">png</option> 35 <option value="png">PNG</option>
38 <option value="eps">eps</option> 36 <option value="eps">EPS</option>
39 <option value="svg">svg</option> 37 <option value="svg">SVG</option>
40 </param> 38 </param>
41 </inputs> 39 </inputs>
42 <outputs> 40 <outputs>
43 <data format="txt" name="output" metadata_source="input" label="BED to IGV on ${input.name}"/> 41 <data name="output" format="txt" metadata_source="input" label="BED to IGV on ${input.name}"/>
44 </outputs> 42 </outputs>
45 <tests> 43 <tests>
46 <test> 44 <test>
47 <param name="input" value="bed12.bed" ftype="bed" /> 45 <param name="input" value="bed12.bed" ftype="bed" />
48 <output name="output" file="igv_bed_script.txt" ftype="txt" /> 46 <output name="output" file="igv_bed_script.txt" ftype="txt" />
49 </test> 47 </test>
50 </tests> 48 </tests>
51 <help> 49 <help><![CDATA[
52 <![CDATA[
53 **What it does** 50 **What it does**
54 51
55 Creates a batch script to create IGV images at each interval defined in a @STD_BEDTOOLS_INPUT_LABEL@ file. 52 Creates a batch script to create IGV images at each interval defined in a @STD_BEDTOOLS_INPUT_LABEL@ file.
56 53
57 **Notes** 54 **Notes**
58 55
59 (1) The resulting script is meant to be run from within IGV. 56 (1) The resulting script is meant to be run from within IGV.
60 (2) It is assumed that prior to running the script, you've loaded the proper genome and tracks. 57 (2) It is assumed that prior to running the script, you've loaded the proper genome and tracks.
61 58
62 @REFERENCES@ 59 @REFERENCES@
63 ]]> 60 ]]></help>
64 </help>
65 <expand macro="citations" /> 61 <expand macro="citations" />
66 </tool> 62 </tool>