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comparison ribotaper_part3_main.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_ribosome_profiling" name="ribotaper part 3: ribosome profiling" version="0.1.0"> 1 <tool id="ribotaper_ribosome_profiling" name="ribotaper part 3: ribosome profiling" 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 tar 11 #if $annotation_path.is_of_type("tgz")
11 "xzvf" 12 tar -xzvf '${annotation_path}' &&
12 "$annotation_path" 13 #else
13 14 tar -xvf '${annotation_path}' &&
14 && 15 #end if
15
16 Ribotaper.sh 16 Ribotaper.sh
17 "$ribo_bam" 17 '${ribo_bam}'
18 "$rna_bam" 18 '${rna_bam}'
19 "annotation_path" 19 './annotation_path'
20 "$read_lenghts_ribo" 20 '${read_lenghts_ribo}'
21 "$cutoff" 21 '${cutoff}'
22 "\${GALAXY_SLOTS:-12}" 22 \${GALAXY_SLOTS:-12}
23
24 ]]></command> 23 ]]></command>
25 <inputs> 24 <inputs>
26 <param name="annotation_path" type="data" format="tar" label="annotation_path" help="Please run 'ribotaper part 1' to generate the archive."/> 25 <param name="annotation_path" type="data" format="tgz,tar" label="Annotation path" help="Please run 'ribotaper part 1' to generate the archive."/>
27 <param name="ribo_bam" type="data" format="BAM" label="ribo_bam" help="Ribo-seq alignment file in BAM format."/> 26 <param name="ribo_bam" type="data" format="BAM" label="Ribo-seq alignment file" help="Ribo-seq alignment file in BAM format."/>
28 <param name="rna_bam" type="data" format="BAM" label="rna_bam" help="RNA-seq alignment file in BAM format."/> 27 <param name="rna_bam" type="data" format="BAM" label="RNA-seq alignment file" help="RNA-seq alignment file in BAM format."/>
29 <param name="read_lenghts_ribo" type="text" value="26,28,29" label="Read length" help="Read lengths, comma-separated values, which are used for P-site calculation. Example, 26,28,29. 28 <param name="read_lenghts_ribo" type="text" value="26,28,29" label="Read length" help="Read lengths, comma-separated values, which are used for P-site calculation. Example, 26,28,29.
30 Please run 'ribotaper part 2' to deterimine appropriate values."/> 29 Please run 'ribotaper part 2' to deterimine appropriate values.">
30 <sanitizer invalid_char="">
31 <valid initial="string.digits">
32 <add value="," />
33 </valid>
34 </sanitizer>
35 <validator type="regex">[0-9,]+</validator>
36 </param>
31 <param name="cutoff" type="text" value="9,12,12" label="Cutoff" help="Cutoffs, comma-separated values, which are used for P-sites calculation. Example, 9,12,12. 37 <param name="cutoff" type="text" value="9,12,12" label="Cutoff" help="Cutoffs, comma-separated values, which are used for P-sites calculation. Example, 9,12,12.
32 Please run 'ribotaper part 2' to deterimine appropriate values."/> 38 Please run 'ribotaper part 2' to deterimine appropriate values.">
39 <sanitizer invalid_char="">
40 <valid initial="string.digits">
41 <add value="," />
42 </valid>
43 </sanitizer>
44 <validator type="regex">[0-9,]+</validator>
45 </param>
33 </inputs> 46 </inputs>
34 <outputs> 47 <outputs>
35 <data name="output1" format="pdf" from_work_dir="quality_check_plots.pdf" label="QC plots"/> 48 <data name="output1" format="pdf" from_work_dir="quality_check_plots.pdf" label="${tool.name} on ${on_string}: QC plots"/>
36 <data name="output2" format="tabular" from_work_dir="ORFs_genes_found" label="Summary of translated ORFs"/> 49 <data name="output2" format="tabular" from_work_dir="ORFs_genes_found" label="${tool.name} on ${on_string}: Summary of translated ORFs"/>
37 <data name="output3" format="tabular" from_work_dir="ORFs_max" label="Translated ORFs (max)"/> 50 <data name="output3" format="tabular" from_work_dir="ORFs_max" label="${tool.name} on ${on_string}: Translated ORFs (max)"/>
38 <data name="output4" format="tabular" from_work_dir="ORFs_max_filt" label="Translated ORFs (max_filt)"/> 51 <data name="output4" format="tabular" from_work_dir="ORFs_max_filt" label="${tool.name} on ${on_string}: Translated ORFs (max_filt)"/>
39 <data name="output5" format="bed" from_work_dir="translated_ORFs_sorted.bed" label="Translated ORFs (sorted)"/> 52 <data name="output5" format="bed" from_work_dir="translated_ORFs_sorted.bed" label="${tool.name} on ${on_string}: Translated ORFs (sorted)"/>
40 <data name="output6" format="bed" from_work_dir="translated_ORFs_filtered_sorted.bed" label="Translated ORFs (filtered/sorted)"/> 53 <data name="output6" format="bed" from_work_dir="translated_ORFs_filtered_sorted.bed" label="${tool.name} on ${on_string}: Translated ORFs (filtered/sorted)"/>
41 <data name="output7" format="fasta" from_work_dir="protein_db_max.fasta" label="Protein DB"/> 54 <data name="output7" format="fasta" from_work_dir="protein_db_max.fasta" label="${tool.name} on ${on_string}: Protein DB"/>
42 <data name="output8" format="pdf" from_work_dir="Final_ORF_results.pdf" label="ORF categories (length/coverage)"/> 55 <data name="output8" format="pdf" from_work_dir="Final_ORF_results.pdf" label="${tool.name} on ${on_string}: ORF categories (length/coverage)"/>
43 </outputs> 56 </outputs>
44 <tests> 57 <tests>
45 <test> 58 <test expect_num_outputs="8">
46 <param name="annotation_path" value="annotation_path.tgz" ftype="tar"/> 59 <param name="annotation_path" value="annotation_path.tgz"/>
47 <param name="ribo_bam" value="test_ribo.bam"/> 60 <param name="ribo_bam" value="test_ribo.bam"/>
48 <param name="rna_bam" value="test_rna.bam"/> 61 <param name="rna_bam" value="test_rna.bam"/>
49 <output name="output2" file="ORFs_genes_found"/> 62 <output name="output2" file="ORFs_genes_found"/>
50 </test> 63 </test>
51 </tests> 64 </tests>
94 107
95 **ORF categories (length/coverage)**: 108 **ORF categories (length/coverage)**:
96 PDF file containing info about the number of ORFs found, together with their length and coverage per category/annotation. 109 PDF file containing info about the number of ORFs found, together with their length and coverage per category/annotation.
97 110
98 ]]></help> 111 ]]></help>
99 <citations> 112 <expand macro="citations"/>
100 <citation type="doi">10.1038/nmeth.3688</citation>
101 </citations>
102 </tool> 113 </tool>