Mercurial > repos > iuc > macs2

comparison macs2_bdgdiff.xml @ 12:38769345062e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 09ef7ee96fadeef22273029ea23d1e140ce96737
author iuc
date Thu, 22 Mar 2018 09:43:37 -0400
parents acbd3fb47f90
children 640d3af5d833
comparison
equal deleted inserted replaced
11:cb785e26207c 12:38769345062e
1 <tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="@VERSION_STRING@.0"> 1 <tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="@VERSION_STRING@.1" profile="17.09">
2 <description>Differential peak detection based on paired four bedgraph files</description> 2 <description>Differential peak detection based on paired four bedgraph files</description>
3 <macros> 3 <macros>
4 <import>macs2_macros.xml</import> 4 <import>macs2_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
21 --depth2 '${ depth.depth2 }' 21 --depth2 '${ depth.depth2 }'
22 --max-gap '${ maxgap }' 22 --max-gap '${ maxgap }'
23 -o c1.bed c2.bed both.bed && 23 -o c1.bed c2.bed both.bed &&
24 24
25 awk '!/^track name/' "c1.bed" > '${ output_cond1 }' && 25 awk '!/^track name/' "c1.bed" > '${ output_cond1 }' &&
26 awk '!/^track name/' "c2.bed" > '${ output_cond1 }' && 26 awk '!/^track name/' "c2.bed" > '${ output_cond2 }' &&
27 awk '!/^track name/' "both.bed" > '${ output_both }' 27 awk '!/^track name/' "both.bed" > '${ output_both }'
28 ]]></command> 28 ]]></command>
29 <inputs> 29 <inputs>
30 <param name="t1" type="data" format="bedgraph" label="BedGraph for Treatment experiment 1" /> 30 <param name="t1" type="data" format="bedgraph" label="BedGraph for Treatment experiment 1" />
31 <param name="t2" type="data" format="bedgraph" label="BedGraph for Treatment experiment 2" /> 31 <param name="t2" type="data" format="bedgraph" label="BedGraph for Treatment experiment 2" />
49 <data name="output_cond2" format="bed" label="${tool.name} on ${on_string} (Condition 2)"/> 49 <data name="output_cond2" format="bed" label="${tool.name} on ${on_string} (Condition 2)"/>
50 <data name="output_both" format="bed" label="${tool.name} on ${on_string} (Common)"/> 50 <data name="output_both" format="bed" label="${tool.name} on ${on_string} (Common)"/>
51 </outputs> 51 </outputs>
52 <tests> 52 <tests>
53 <test> 53 <test>
54
55 <param name="t1" value="bdgdiff_t1.bdg" ftype="bedgraph"/> 54 <param name="t1" value="bdgdiff_t1.bdg" ftype="bedgraph"/>
56 <param name="t2" value="bdgdiff_t2.bdg" ftype="bedgraph"/> 55 <param name="t2" value="bdgdiff_t2.bdg" ftype="bedgraph"/>
57 <param name="c1" value="bdgdiff_c1.bdg" ftype="bedgraph"/> 56 <param name="c1" value="bdgdiff_c1.bdg" ftype="bedgraph"/>
58 <param name="c2" value="bdgdiff_c2.bdg" ftype="bedgraph"/> 57 <param name="c2" value="bdgdiff_c2.bdg" ftype="bedgraph"/>
59 <param name="cutoff" value="1.0"/> 58 <param name="cutoff" value="1.0"/>
60 <param name="minlen" value="200"/> 59 <param name="minlen" value="200"/>
61 <param name="depth1" value="10"/> 60 <param name="depth1" value="10"/>
62 <param name="depth2" value="1"/> 61 <param name="depth2" value="1"/>
63 <param name="maxgap" value="100"/> 62 <param name="maxgap" value="100"/>
64 <output name="output_cond1"> 63 <output name="output_cond1" ftype="bed" value="bdgdiff_output_c1.bed"/>
64 <output name="output_cond2">
65 <assert_contents> 65 <assert_contents>
66 <has_text text="c2.bed1" /> 66 <has_text text="c2.bed1" />
67 </assert_contents> 67 </assert_contents>
68 </output> 68 </output>
69 <output name="output_both" ftype="bed" value="bdgdiff_output_both.bed"/>
69 </test> 70 </test>
70 </tests> 71 </tests>
71 <help> 72 <help>
72 <![CDATA[ 73 <![CDATA[
73 **What it does** 74 **What it does**