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comparison hicup_digester.xml @ 5:2edfb71706b3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
author bgruening
date Sat, 22 Oct 2022 08:41:11 +0000
parents a2f3a4129052
children e79c38f1752c
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4:a2f3a4129052 5:2edfb71706b3
1 <tool id="hicup_digester" name="Hicup Digester" version="@VERSION@.0"> 1 <tool id="hicup_digester" name="Hicup Digester" version="@VERSION@+galaxy0">
2 <description>cuts throughout a selected genome at one or two specified restriction sites.</description> 2 <description>cuts throughout a selected genome at one or two specified restriction sites.</description>
3 <macros> 3 <macros>
4 <import>hicup_macros.xml</import> 4 <import>hicup_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements_hicup" /> 6 <expand macro="requirements_hicup" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 hicup_digester --re1 '$re1' --genome '$genome' 8 hicup_digester --re1 '$re1' --genome '$genome'
9 #if $advanced_options.re2: 9 #if $advanced_options.re2:
10 --re2 '$advanced_options.re2' 10 --re2 '$advanced_options.re2'
11 #end if 11 #end if
12 #for $file in $input_files_digest: 12 #if str($input_files_digest.source) == "history":
13 $file 13 #for $file in $input_files_digest.own_file:
14 #end for 14 '$file'
15 #end for
16 #else:
17 '$reference_genome.index.fields.path'.fa
18 #end if
15 ]]></command> 19 ]]></command>
16 <inputs> 20 <inputs>
17 <param name="input_files_digest" type="data" multiple="true" format="fasta" label="Input DNA sequence files that should be digested"/> 21 <conditional name="input_files_digest">
22 <param name="source" type="select" label="Will you select a reference genome from your history or use a genome which has a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
23 <option value="indexed">Use a genome with a built-in index</option>
24 <option value="history">Use a genome from the history</option>
25 </param>
26 <when value="indexed">
27 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
28 <options from_data_table="bowtie2_indexes">
29 <filter type="sort_by" column="2"/>
30 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
31 </options>
32 </param>
33 </when>
34 <when value="history">
35 <param name="own_file" type="data" format="fasta" multiple="true" label="Select reference genome" />
36 <!--<param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />-->
37 </when>
38 </conditional>
18 <param argument="--genome" type="text" label="Genome name" 39 <param argument="--genome" type="text" label="Genome name"
19 help="Name of the genome to be digested."/> 40 help="Name of the genome to be digested."/>
20 <expand macro="re1" /> 41 <expand macro="re1" />
21 <section name="advanced_options" title="Advanced options"> 42 <section name="advanced_options" title="Advanced options">
22 <expand macro="re2" /> 43 <expand macro="re2" />
23 </section> 44 </section>
24 </inputs> 45 </inputs>
25 <outputs> 46 <outputs>
26 <data name="digest_file" format="txt" from_work_dir="Digest_*" label="Digester File.txt"/> 47 <data name="digest_file" format="tabular" from_work_dir="Digest_*" label="Digester File.txt"/>
27 </outputs> 48 </outputs>
28 <tests> 49 <tests>
29 <test> 50 <test>
30 <param name="input_files_digest" value="chr21And22FromHg38.fasta"/> 51 <param name="source" value="history"/>
52 <param name="own_file" value="chr21And22FromHg38.fasta"/>
31 <param name="re1" value="A^AGCTT"/> 53 <param name="re1" value="A^AGCTT"/>
32 <param name="genome" value="chr21And22FromHg38"/> 54 <param name="genome" value="chr21And22FromHg38"/>
33 <output name="digest_file" file="digester_file.txt" lines_diff="4"/> 55 <output name="digest_file" file="digester_file.txt" lines_diff="0"/>
34 </test> 56 </test>
35 </tests> 57 </tests>
36 <help><![CDATA[ 58 <help><![CDATA[
37 59
38 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/ 60 For help please consult the documentation of HiCUP: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html
39 61
40 To get more information about the digister visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Digester 62 To get more information about the digister visit:https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html#hicup-digester
41 ]]></help> 63 ]]></help>
42 <expand macro="citation_hicup" /> 64 <expand macro="citation_hicup" />
43 </tool> 65 </tool>