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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 398a2e3e845ada656b3a7e0a6542e1668a8bcf17
author bgruening
date Thu, 23 Feb 2023 18:01:57 +0000
parents 2edfb71706b3
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1 <tool id="hicup_digester" name="Hicup Digester" version="@VERSION@+galaxy0">
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2 <description>cuts throughout a selected genome at one or two specified restriction sites.</description>
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3 <macros>
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4 <import>hicup_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements_hicup" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 hicup_digester --re1 '$re1' --genome '$genome'
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9 #if $advanced_options.re2:
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10 --re2 '$advanced_options.re2'
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11 #end if
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12 #if str($input_files_digest.source) == "history":
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13 #for $file in $input_files_digest.own_file:
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14 '$file'
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15 #end for
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16 #else:
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17 '$reference_genome.index.fields.path'.fa
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18 #end if
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19 ]]></command>
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20 <inputs>
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21 <conditional name="input_files_digest">
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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">
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23 <option value="indexed">Use a genome with a built-in index</option>
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24 <option value="history">Use a genome from the history</option>
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25 </param>
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26 <when value="indexed">
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27 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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28 <options from_data_table="bowtie2_indexes">
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29 <filter type="sort_by" column="2"/>
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30 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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31 </options>
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32 </param>
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33 </when>
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34 <when value="history">
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35 <param name="own_file" type="data" format="fasta" multiple="true" label="Select reference genome" />
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36 <!--<param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />-->
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37 </when>
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38 </conditional>
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39 <param argument="--genome" type="text" label="Genome name"
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40 help="Name of the genome to be digested."/>
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41 <expand macro="re1" />
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42 <section name="advanced_options" title="Advanced options">
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43 <expand macro="re2" />
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44 </section>
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45 </inputs>
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46 <outputs>
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47 <data name="digest_file" format="tabular" from_work_dir="Digest_*" label="Digester File.txt"/>
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="source" value="history"/>
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52 <param name="own_file" value="chr21And22FromHg38.fasta"/>
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53 <param name="re1" value="A^AGCTT"/>
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54 <param name="genome" value="chr21And22FromHg38"/>
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55 <output name="digest_file" file="digest_file.txt" lines_diff="0"/>
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56 </test>
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57 </tests>
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58 <help><![CDATA[
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59
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60 For help please consult the documentation of HiCUP: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html
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61
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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
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63 ]]></help>
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64 <expand macro="citation_hicup" />
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65 </tool>