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comparison tradis_gene_insert_sites.xml @ 1:58234d95978d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 61c83ac999a040604915ff7cf92670b2635b967e"
author iuc
date Fri, 07 Feb 2020 05:20:39 -0500
parents 738e58ed9cc2
children 103bd59b3e33
comparison
equal deleted inserted replaced
0:738e58ed9cc2 1:58234d95978d
1 <tool id="tradis_gene_insert_sites" name="Bio-TraDis counts to gene insertion data" version="@VERSION@"> 1 <tool id="tradis_gene_insert_sites" name="Bio-TraDis counts to gene insertion data" version="@TOOL_VERSION@+galaxy@VERSION@">
2 <description></description> 2 <description></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" />
10 ]]> 10 ]]>
11 </command> 11 </command>
12 12
13 <inputs> 13 <inputs>
14 <param name="input_counts" type="data" format="tabular" label="Read counts" help="Read counts at each nucleotide position for both strands. The first column contains forward strand counts, and the second contains reverse strand counts."/> 14 <param name="input_counts" type="data" format="tabular" label="Read counts" help="Read counts at each nucleotide position for both strands. The first column contains forward strand counts, and the second contains reverse strand counts."/>
15 <param name="input_annot" type="data" format="txt" label="EMBL file containing the reference genome annotations"/> 15 <param name="input_annot" type="data" format="embl" label="EMBL file containing the reference genome annotations"/>
16 <param name="trim3" type="float" value="0.1" min="0" max="1" label="Portion of the gene to trim in 3' end'" help="Trim reads at the 3'end of genes. Some transposon insertions can be little disruptive when they occur end of genes. Trim to ignore these reads."/> 16 <param name="trim3" type="float" value="0.1" min="0" max="1" label="Portion of the gene to trim in 3' end'" help="Trim reads at the 3'end of genes. Some transposon insertions can be little disruptive when they occur end of genes. Trim to ignore these reads."/>
17 <param name="trim5" type="float" value="0" min="0" max="1" label="Portion of the gene to trim" help="Trim reads at the 5'end of genes. Some transposon insertions can be little disruptive when they occur end of genes. Trim to ignore these reads."/> 17 <param name="trim5" type="float" value="0" min="0" max="1" label="Portion of the gene to trim" help="Trim reads at the 5'end of genes. Some transposon insertions can be little disruptive when they occur end of genes. Trim to ignore these reads."/>
18 18
19 </inputs> 19 </inputs>
20 20
21 <outputs> 21 <outputs>
22 <data name="gene_insert_sites" format="csv" from_work_dir="./*.csv"/> 22 <data name="gene_insert_sites" format="csv" from_work_dir="./*.csv" label="${tool.name} on ${on_string}"/>
23 </outputs> 23 </outputs>
24 24
25 <tests> 25 <tests>
26 <test> 26 <test>
27 <param name="input_counts" ftype="tabular" value="tiny.out.gz.CP009273.1_60_120.insert_site_plot.gz"/> 27 <param name="input_counts" ftype="tabular" value="tiny.out.gz.CP009273.1_60_120.insert_site_plot.gz"/>
28 <param name="input_annot" ftype="txt" value="tiny_ref.embl"/> 28 <param name="input_annot" ftype="embl" value="tiny_ref.embl"/>
29 <param name="trim3" ftype="float" value="0"/> 29 <param name="trim3" ftype="float" value="0"/>
30 <param name="trim5" ftype="float" value="0"/> 30 <param name="trim5" ftype="float" value="0"/>
31 <output name="gene_insert_sites" file="tiny.out.gz.CP009273.1_60_120.tradis_gene_insert_sites.csv" compare="sim_size" delta="200" /> 31 <output name="gene_insert_sites" file="tiny.out.gz.CP009273.1_60_120.tradis_gene_insert_sites.csv" compare="sim_size" delta="200" />
32 </test> 32 </test>
33 </tests> 33 </tests>
71 71
72 </tool> 72 </tool>
73 73
74 74
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