Mercurial > repos > rnateam > ribotaper

comparison ribotaper_part2_create_metaplots.xml @ 3:579b3be2559f draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit cd589d3c7c1bbe02e924f73475156c4f140d2fe2"
author rnateam
date Fri, 03 Jun 2022 20:17:28 +0000
parents 9dda0cc9ff98
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2:9dda0cc9ff98 3:579b3be2559f
1 <tool id="ribotaper_create_metaplots" name="ribotaper part 2: metagene analysis for P-sites definition" version="0.1.0"> 1 <tool id="ribotaper_create_metaplots" name="ribotaper part 2: metagene analysis for P-sites definition" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile='20.01'>
2 <requirements> 2 <macros>
3 <requirement type="package" version="1.3.1a">ribotaper</requirement> 3 <import>macros.xml</import>
4 </requirements> 4 </macros>
5 <expand macro='bio_tools'/>
6 <expand macro='requirements'/>
5 <stdio> 7 <stdio>
6 <exit_code range="1:" /> 8 <exit_code range="1:" />
7 </stdio> 9 </stdio>
8
9 <command><![CDATA[ 10 <command><![CDATA[
10 create_metaplots.bash 11 create_metaplots.bash
11 "$ribo_bam" 12 "$ribo_bam"
12 "$start_stops_FAR" 13 "$start_stops_FAR"
13 "metagene" 14 "metagene"
14
15 && 15 &&
16
17 find "metaplots" 16 find "metaplots"
18 "-name" 17 "-name"
19 "metagene*.pdf" 18 "metagene*.pdf"
20 | sort | xargs gs 19 | sort | xargs gs
21 "-dAutoRotatePages=/None" 20 "-dAutoRotatePages=/None"
22 "-dBATCH" 21 "-dBATCH"
23 "-dNOPAUSE" 22 "-dNOPAUSE"
24 "-q" 23 "-q"
25 "-sDEVICE=pdfwrite" 24 "-sDEVICE=pdfwrite"
26 "-sOutputFile=merged_metagene.pdf" 25 "-sOutputFile=merged_metagene.pdf"
27
28 ]]></command> 26 ]]></command>
29 <inputs> 27 <inputs>
30 <param name="ribo_bam" type="data" format="bam" label="ribo_bam" help="Ribo-seq alignment file in BAM format."/> 28 <param name="ribo_bam" type="data" format="bam" label="Ribo-seq alignment file" help="Ribo-seq alignment file in BAM format."/>
31 <param name="start_stops_FAR" type="data" format="bed" label="start_stops_FAR" help="Please run 'ribotaper part 1' to generate the table."/> 29 <param name="start_stops_FAR" type="data" format="bed" label="Start_stops FAR" help="Please run 'ribotaper part 1' to generate the table."/>
32 </inputs> 30 </inputs>
33 <outputs> 31 <outputs>
34 <data name="output1" format="pdf" from_work_dir="merged_metagene.pdf" label="Metagene analysis results for P-sites definition (figures)"/> 32 <data name="output1" format="pdf" from_work_dir="merged_metagene.pdf" label="${tool.name} on ${on_string}: Metagene analysis results for P-sites definition (figures)"/>
35 <data name="output2" format="tabular" from_work_dir="metagene" label="Metagene analysis results for P-sites definition (table)"/> 33 <data name="output2" format="tabular" from_work_dir="metagene" label="${tool.name} on ${on_string}: Metagene analysis results for P-sites definition (table)"/>
36 </outputs> 34 </outputs>
37 <tests> 35 <tests>
38 <test> 36 <test expect_num_outputs="2">
39 <param name="ribo_bam" value="test_ribo.bam" ftype="bam"/> 37 <param name="ribo_bam" value="test_ribo.bam" ftype="bam"/>
40 <param name="start_stops_FAR" value="annotation_path/start_stops_FAR.bed" ftype="bed"/> 38 <param name="start_stops_FAR" value="annotation_path/start_stops_FAR.bed" ftype="bed"/>
41 <output name="output2" file="metagene"/> 39 <output name="output2" file="metagene"/>
42 </test> 40 </test>
43 </tests> 41 </tests>
85 From the output, user shall determine the appropriate 83 From the output, user shall determine the appropriate
86 read lengths and cutoffs which are required 84 read lengths and cutoffs which are required
87 for running ``ribotaper part 3``, ribosome profiling. 85 for running ``ribotaper part 3``, ribosome profiling.
88 86
89 ]]></help> 87 ]]></help>
90 <citations> 88 <expand macro="citations"/>
91 <citation type="doi">10.1038/nmeth.3688</citation>
92 </citations>
93 </tool> 89 </tool>