Mercurial > repos > petr-novak > repeat_annotation_pipeline3
comparison format_repeat_library.xml @ 11:5366d5ea04bc draft
planemo upload commit 9d1b19f98d8b7f0a0d1baf2da63a373d155626f8-dirty
author | petr-novak |
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date | Fri, 04 Aug 2023 12:35:32 +0000 |
parents | ea6a3059a6af |
children |
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10:276efc4cb17f | 11:5366d5ea04bc |
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1 <tool id="annotate_contigs" name="Format Repeat Library" version="0.1.0" python_template_version="3.5"> | 1 <tool id="annotate_contigs" name="Format Repeat Library" version="0.1.0" python_template_version="3.5"> |
2 <requirements> | 2 <requirements> |
3 <requirement type="package" version="2.60.0">bioconductor-biostrings</requirement> | 3 <requirement type="package" version="2.60.0">bioconductor-biostrings</requirement> |
4 </requirements> | 4 </requirements> |
5 <required_files> | |
6 <include type="literal" path="annotate_contigs.R"/> | |
7 </required_files> | |
5 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
6 $__tool_directory__/annotate_contigs.R '$contigs' '$cluster_table' '$annotated_contigs' | 9 Rscript $__tool_directory__/annotate_contigs.R '$contigs' '$cluster_table' '$annotated_contigs' |
7 ]]></command> | 10 ]]></command> |
8 <inputs> | 11 <inputs> |
9 <param type="data" name="contigs" format="fasta" label="Contigs - Library of Repeats from TAREAN/RepeatExplorer pipeline" /> | 12 <param type="data" name="contigs" format="fasta" label="Contigs - Library of Repeats from TAREAN/RepeatExplorer pipeline" /> |
10 <param type="data" name="cluster_table" format="txt" label="CLUSTER_TABLE from RepeatExplorer pipeline" help="CLUSTER_TABLE which contain annotation of clusters from RepeatExplorer pipeline"/> | 13 <param type="data" name="cluster_table" format="txt" label="CLUSTER_TABLE from RepeatExplorer pipeline" help="CLUSTER_TABLE which contain annotation of clusters from RepeatExplorer pipeline"/> |
11 </inputs> | 14 </inputs> |
58 | 61 |
59 Only Cluster, Automatic_annotation/Final_annnotation are mandatory" | 62 Only Cluster, Automatic_annotation/Final_annnotation are mandatory" |
60 | 63 |
61 Clusters with higher number than those in CLUSTER_TABLE are removed from Repeat library | 64 Clusters with higher number than those in CLUSTER_TABLE are removed from Repeat library |
62 | 65 |
63 Contigs are provided in followinf format:: | 66 Contigs are provided in following format:: |
64 | 67 |
65 | 68 |
66 >CL25Contig1 | 69 >CL25Contig1 |
67 AGATCAAGATGGCGCCGGAGGACATGGAGAAAACGACGTTTATCACTCCCTGGGGAACATTTTGCTACAAGGTAATGCCT | 70 AGATCAAGATGGCGCCGGAGGACATGGAGAAAACGACGTTTATCACTCCCTGGGGAACATTTTGCTACAAGGTAATGCCT |
68 TTCGGTCTGAAGAACGCAGGGGCCACTTACCAACGAGCAATGGTAACTT | 71 TTCGGTCTGAAGAACGCAGGGGCCACTTACCAACGAGCAATGGTAACTT |