Mercurial > repos > thanhlv > polypolish

annotate polypolish.xml @ 1:a38f6a0ebbf9 draft

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"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polypolish commit f361210f97bf2dfa63c2267193eca3163e17f78a-dirty"
author thanhlv
date Fri, 23 Sep 2022 23:26:59 +0000
parents 3c7cbfb8f43d
children 96580cd76488
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3c7cbfb8f43d "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polypolish commit e855ff93b8b8493f8f061895d111885b938655e8-dirty"
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1 <tool id="polypolish" name="polypolish" version="@VERSION@">
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2 <description> Polishing genome assemblies with short reads</description>
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3 <macros>
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4 <token name="@VERSION@">0.5.0</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">polypolish</requirement>
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8 <!--<requirement type="package" version="1.15.1">samtools</requirement> -->
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9 <requirement type="package" version="0.7.17">bwa</requirement>
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10 </requirements>
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11 <version_command>polypolish --version</version_command>
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12 <command detect_errors="exit_code"><![CDATA[
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13 #if $short_reads.sr_type == 'paired'
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14 ln -s '$short_reads.R1' reads_1.fastq.gz &&
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15 ln -s '$short_reads.R2' reads_2.fastq.gz &&
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16 #else if str($short_reads.sr_type) == "collection"
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17 ln -s '$short_reads.input1.forward' reads_1.fastq.gz &&
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18 ln -s '$short_reads.input1.reverse' reads_2.fastq.gz &&
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19 #end if
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20
0
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21 ln -s '${assembly}' draft.fa &&
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22 bwa index draft.fa &&
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23 bwa mem -t \${GALAXY_SLOTS:-4} -a draft.fa reads_1.fastq.gz > alignments_1.sam &&
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24 bwa mem -t \${GALAXY_SLOTS:-4} -a draft.fa reads_2.fastq.gz > alignments_2.sam &&
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25 polypolish_insert_filter.py --in1 alignments_1.sam --in2 alignments_2.sam --out1 filtered_1.sam --out2 filtered_2.sam &&
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a38f6a0ebbf9 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polypolish commit f361210f97bf2dfa63c2267193eca3163e17f78a-dirty"
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26 polypolish
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27 #if $debug
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28 $debug debug.tsv
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29 #end if
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30 -d ${min_depth}
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31 -i ${fraction_invalid}
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32 -m ${max_errors}
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33 -v ${fraction_valid}
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34 draft.fasta filtered_1.sam filtered_2.sam
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35 > polished.fasta
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36 ]]> </command>
3c7cbfb8f43d "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polypolish commit e855ff93b8b8493f8f061895d111885b938655e8-dirty"
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37
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38 <inputs>
1
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39 <param name="assembly" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Assembly"/>
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40 <conditional name="short_reads">
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41 <param name="sr_type" type="select" label="Input reads type or collection" help="Select 'paired end' for a single library or 'collection' for a paired end collection">
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42 <option value="paired" selected="true">Paired End</option>
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43 <option value="collection">Paired Collection</option>
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44 </param>
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45 <when value="paired">
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46 <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
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47 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
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48 </when>
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49 <when value="collection">
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50 <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/>
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51 </when>
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52 </conditional>
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53 <param argument="min_depth" type="integer" value="5" min="1" label="Minimum depth" />
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54 <param argument="fraction_invalid" type="float" value="0.2" min="0.0" max="1.0" label="Fraction value of the read depth to be considered invalid" />
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55 <param argument="fraction_valid" type="integer" value="0.2" min="0.0" max="1.0" label="Ignore alignments with more than this many mismatches and indels" />
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56 <param argument="max_errors" type="integer" value="10" min="1" label="Fraction value of the read depth to be considered invalid" />
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57 <param argument="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Debug output" />
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58 </inputs>
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59 <outputs>
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60 <data name="polished" format="fasta" from_work_dir="polished.fasta" label="${tool.name} on ${on_string} Polished assembly" />
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61 <data name="debug" format="tabular" from_work_dir="debug.tsv" label="${tool.name} on ${on_string} Polished assembly" >
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62 <filter>debug is True</filter>
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63 </data>
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64 </outputs>
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65 <help><![CDATA[
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66 ]]> </help>
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67 </tool>