Mercurial > repos > rnateam > ribotaper

comparison ribotaper_part3_main.xml @ 2:9dda0cc9ff98 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
author rnateam
date Wed, 30 Nov 2016 16:57:07 -0500
parents a56343c142d5
children 579b3be2559f
comparison
equal deleted inserted replaced
1:a56343c142d5 2:9dda0cc9ff98
21 "$cutoff" 21 "$cutoff"
22 "\${GALAXY_SLOTS:-12}" 22 "\${GALAXY_SLOTS:-12}"
23 23
24 ]]></command> 24 ]]></command>
25 <inputs> 25 <inputs>
26 <param name="annotation_path" type="data" format="zip" label="annotation_path" help="Please run 'ribotaper part 1' to generate the archive."/> 26 <param name="annotation_path" type="data" format="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."/> 27 <param name="ribo_bam" type="data" format="BAM" label="ribo_bam" 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."/> 28 <param name="rna_bam" type="data" format="BAM" label="rna_bam" 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. 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.
30 Please run 'ribotaper part 2' to deterimine appropriate values."/> 30 Please run 'ribotaper part 2' to deterimine appropriate values."/>
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. 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.
32 Please run 'ribotaper part 2' to deterimine appropriate values."/> 32 Please run 'ribotaper part 2' to deterimine appropriate values."/>
33 </inputs> 33 </inputs>
34 <outputs> 34 <outputs>
35 <data name="output1" type="data" format="pdf" from_work_dir="quality_check_plots.pdf" label="QC plots"/> 35 <data name="output1" format="pdf" from_work_dir="quality_check_plots.pdf" label="QC plots"/>
36 <data name="output2" type="data" format="tabular" from_work_dir="ORFs_genes_found" label="Summary of translated ORFs"/> 36 <data name="output2" format="tabular" from_work_dir="ORFs_genes_found" label="Summary of translated ORFs"/>
37 <data name="output3" type="data" format="tabular" from_work_dir="ORFs_max" label="Translated ORFs (max)"/> 37 <data name="output3" format="tabular" from_work_dir="ORFs_max" label="Translated ORFs (max)"/>
38 <data name="output4" type="data" format="tabular" from_work_dir="ORFs_max_filt" label="Translated ORFs (max_filt)"/> 38 <data name="output4" format="tabular" from_work_dir="ORFs_max_filt" label="Translated ORFs (max_filt)"/>
39 <data name="output5" type="data" format="bed" from_work_dir="translated_ORFs_sorted.bed" label="Translated ORFs (sorted)"/> 39 <data name="output5" format="bed" from_work_dir="translated_ORFs_sorted.bed" label="Translated ORFs (sorted)"/>
40 <data name="output6" type="data" format="bed" from_work_dir="translated_ORFs_filtered_sorted.bed" label="Translated ORFs (filtered/sorted)"/> 40 <data name="output6" format="bed" from_work_dir="translated_ORFs_filtered_sorted.bed" label="Translated ORFs (filtered/sorted)"/>
41 <data name="output7" type="data" format="fasta" from_work_dir="protein_db_max.fasta" label="Protein DB"/> 41 <data name="output7" format="fasta" from_work_dir="protein_db_max.fasta" label="Protein DB"/>
42 <data name="output8" type="data" format="pdf" from_work_dir="Final_ORF_results.pdf" label="ORF categories (length/coverage)"/> 42 <data name="output8" format="pdf" from_work_dir="Final_ORF_results.pdf" label="ORF categories (length/coverage)"/>
43 </outputs> 43 </outputs>
44 <tests> 44 <tests>
45 <test> 45 <test>
46 <param name="annotation_path" value="annotation_path.tgz" ftype="zip"/> 46 <param name="annotation_path" value="annotation_path.tgz" ftype="tar"/>
47 <param name="ribo_bam" value="test_ribo.bam"/> 47 <param name="ribo_bam" value="test_ribo.bam"/>
48 <param name="rna_bam" value="test_rna.bam"/> 48 <param name="rna_bam" value="test_rna.bam"/>
49 <output name="output2" file="ORFs_genes_found"/> 49 <output name="output2" file="ORFs_genes_found"/>
50 </test> 50 </test>
51 </tests> 51 </tests>