Mercurial > repos > iuc > macs2
comparison macs2_bdgdiff.xml @ 12:38769345062e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 09ef7ee96fadeef22273029ea23d1e140ce96737
author | iuc |
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date | Thu, 22 Mar 2018 09:43:37 -0400 |
parents | acbd3fb47f90 |
children | 640d3af5d833 |
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11:cb785e26207c | 12:38769345062e |
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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** |