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annotate hicup_macros.xml @ 4:17f80a8600ac draft

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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
author bgruening
date Fri, 25 May 2018 17:50:43 -0400
parents 7e21a0b8d48c
children 30b199ed897d
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1 <macros>
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2 <token name="@VERSION@">0.6.1</token>
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3 <xml name="requirements_hicup">
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4 <requirements>
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5 <requirement type="package" version="@VERSION@">hicup</requirement>
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6 <requirement type="package" version="2.2.6">bowtie2</requirement>
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7 <requirement type="package" version="1.2">samtools</requirement>
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8 <requirement type="package" version="0.13.1">docutils</requirement>
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9 <yield/>
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10 </requirements>
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11 <version_command>hicup --version</version_command>
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12 </xml>
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13 <xml name="citation_hicup">
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14 <citations>
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15 <citation type="doi">10.12688/f1000research.7334.1</citation>
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16 </citations>
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17 </xml>
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18 <xml name="reference_genome_macro">
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19 <conditional name="reference_genome">
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20 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
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21 <option value="indexed">Use a built-in genome index</option>
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22 <option value="history">Use a genome from the history and build index</option>
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23 </param>
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24 <when value="indexed">
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25 <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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26 <options from_data_table="bowtie2_indexes">
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27 <filter type="sort_by" column="2"/>
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28 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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29 </options>
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30 </param>
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31 </when>
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32 <when value="history">
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33 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
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34 <!--<param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />-->
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35 </when>
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36 </conditional>
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37 </xml>
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38 <xml name="input_files">
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39 <param name="input_first_sequence" type="data" format="fastq,fastq.gz" label="First input sequence" help="The first sequence:"/>
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40 <param name="input_second_sequence" type="data" format="fastq,fastq.gz" label="Second input sequence" help="The second sequence:"/>
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41 </xml>
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42 <xml name="re1">
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43 <param argument="--re1" type="text" value="" label="Restriction enzyme recognition sequence" help="Restriction enzyme recognition sequence"/>
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44 </xml>
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45 <xml name="re2">
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46 <param argument="--re2" type="text" value="" label="Restriction enzyme instead of sonication to shorten di-tags."
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47 help="To specify a restriction enzyme instead of sonication to shorten di-tags. This restriction site does NOT form a Hi-C ligation junction. 2 .g. AG^CT,AluI. Typically the sonication protocol is followed."/>
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48 </xml>
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49 <xml name="filter_longest_shortest">
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50 <param argument="--longest" type="text" value="" label="Max insert size" help="Maximum allowable insert size (bps)"/>
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51 <param argument="--shortest" type="text" value="" label="Min insert size" help="Minimum allowable insert size (bps)"/>
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52 </xml>
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53 <xml name="no_fill">
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54 <param argument="--nofill" type="boolean" value="false" truevalue="--nofill" falsevalue="" label="No fill"
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55 help="Hi-C protocol did NOT include a fill-in of sticky ends prior to re-ligation and therefore reads shall be truncated at the restriction site sequence"/>
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56 </xml>
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57 </macros>