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comparison intervene_pairwise.xml @ 3:21beb30956c2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit f0241966e9185e5960947d12dcb490cce1fc6301
author iuc
date Fri, 21 Oct 2022 16:07:46 +0000
parents 33b8c5eedc04
children
comparison
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2:33b8c5eedc04 3:21beb30956c2
1 <tool id="intervene_pairwise" name="Pairwise intersection" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="intervene_pairwise" name="Pairwise intersection" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>and heatmap for genomic intervals</description> 2 <description>and heatmap for genomic intervals</description>
3 <xrefs> 3 <xrefs>
4 <xref type="bio.tools">intervene</xref> 4 <xref type="bio.tools">intervene</xref>
5 </xrefs> 5 </xrefs>
6 <macros> 6 <macros>
15 #set $type = 'genomic 'if $input[0].is_of_type('interval') else 'list' 15 #set $type = 'genomic 'if $input[0].is_of_type('interval') else 'list'
16 intervene pairwise 16 intervene pairwise
17 --type $type 17 --type $type
18 --input #echo " ".join(["'%s'" % file for file in $input]) 18 --input #echo " ".join(["'%s'" % file for file in $input])
19 --names $labels 19 --names $labels
20 --compute $compute 20 --compute $compute_conditional.compute
21 #if $compute_conditional.compute == 'fisher'
22 --genome '$compute_conditional.genome'
23 #end if
21 #if str($corrtype) != 'None' 24 #if str($corrtype) != 'None'
22 --corr 25 --corr
23 --corrtype $corrtype 26 --corrtype $corrtype
24 #end if 27 #end if
25 --htype $htype 28 --htype $htype
33 --dpi $dpi && 36 --dpi $dpi &&
34 mv results/Intervene_pairwise_*.${figtype} results/Intervene_pairwise.plot 37 mv results/Intervene_pairwise_*.${figtype} results/Intervene_pairwise.plot
35 ]]></command> 38 ]]></command>
36 <inputs> 39 <inputs>
37 <param argument="--input" type="data" format="interval" multiple="true" label="Select input files for which to produce intersections"/> 40 <param argument="--input" type="data" format="interval" multiple="true" label="Select input files for which to produce intersections"/>
38 <param argument="--compute" type="select" label="Use this metric for the heatmap"> 41 <conditional name="compute_conditional">
39 <option value="count">count: calculates the number of overlaps</option> 42 <param argument="--compute" type="select" label="Use this metric for the heatmap">
40 <option value="frac" selected="true">frac: calculates the fraction of overlap</option> 43 <option value="count">count: calculates the number of overlaps</option>
41 <option value="jaccard">jaccard: calculate the Jaccard statistic</option> 44 <option value="frac" selected="true">frac: calculates the fraction of overlap</option>
42 <option value="reldist">reldist: calculate the distribution of relative distances</option> 45 <option value="jaccard">jaccard: calculate the Jaccard statistic</option>
43 <!-- fisher option needs additional genome assembly, probably triggers on demand download 46 <option value="reldist">reldist: calculate the distribution of relative distances</option>
44 <option value="fisher">fisher: calculate Fisher`s statistic</option> 47 <option value="fisher">fisher: calculate Fisher`s statistic</option>
45 --> 48 </param>
46 </param> 49 <when value="count"/>
50 <when value="frac"/>
51 <when value="jaccard"/>
52 <when value="reldist"/>
53 <when value="fisher">
54 <param argument="--genome" type="text" value="" label="Reference genome ID" help="Needs to be a string assembly name such as mm10 or hg38">
55 <sanitizer invalid_char="">
56 <valid initial="string.letters,string.digits">
57 </valid>
58 </sanitizer>
59 <validator type="regex">[0-9a-zA-Z]+</validator>
60 </param>
61 </when>
62 </conditional>
47 <param argument="--corrtype" type="select" label="Select the type of correlation"> 63 <param argument="--corrtype" type="select" label="Select the type of correlation">
48 <option value="None">Don't calculate correlation</option> 64 <option value="None">Don't calculate correlation</option>
49 <option value="pearson">Pearson correlation</option> 65 <option value="pearson">Pearson correlation</option>
50 <option value="kendall">Kendall correlation</option> 66 <option value="kendall">Kendall correlation</option>
51 <option value="spearman">Spearman correlation</option> 67 <option value="spearman">Spearman correlation</option>
90 <param name="input" value="a.bed,b.bed,c.bed"/> 106 <param name="input" value="a.bed,b.bed,c.bed"/>
91 <param name="out_matrix" value="true"/> 107 <param name="out_matrix" value="true"/>
92 <output name="plot" value="bed_pairwise.pdf" compare="sim_size"/> 108 <output name="plot" value="bed_pairwise.pdf" compare="sim_size"/>
93 <output name="matrix" value="matrix.txt" /> 109 <output name="matrix" value="matrix.txt" />
94 </test> 110 </test>
111 <!-- Test fisher option -->
112 <test expect_num_outputs="1">
113 <param name="input" value="a.bed,b.bed,c.bed"/>
114 <conditional name="compute_conditional">
115 <param name="compute" value="fisher"/>
116 <param name="genome" value="mm10"/>
117 </conditional>
118 <output name="plot" value="bed_pairwise_fisher.pdf" compare="sim_size"/>
119 </test>
95 </tests> 120 </tests>
96 <help><![CDATA[ 121 <help><![CDATA[
97 **What it does** 122 **What it does**
98 123
99 Plots the pairwise intersections of multiple interval files. 124 Plots the pairwise intersections of multiple interval files.