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comparison ribotaper_part2_create_metaplots.xml @ 1:56ffbec351b3 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 07674fe3507909d11d7431e3b8c48afcfb1f4b5e"
author rnateam
date Tue, 07 Jun 2022 09:22:45 +0000
parents bade631353d2
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0:bade631353d2 1:56ffbec351b3
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>