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comparison assembly_stats_txt.xml @ 1:7556309ffbaf draft default tip

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"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit fb4c29f720748f46ff501140f2cd306bab6614f9"
author nml
date Fri, 29 May 2020 13:51:50 -0400
parents ad2b274663f8
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0:ad2b274663f8 1:7556309ffbaf
1 <tool id="assemblystats" name="assemblystats" version="1.0.1"> 1 <tool id="assemblystats" name="assemblystats" version="1.1.0">
2 <description>Summarise an assembly (e.g. N50 metrics)</description> 2 <description>Summarise an assembly (e.g. N50 metrics)</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.6.924">perl-bioperl</requirement> 4 <requirement type="package" version="1.7.2">perl-bioperl</requirement>
5 <requirement type="package" version="5.0.4">gnuplot</requirement> 5 <requirement type="package" version="5.2.7">gnuplot</requirement>
6 <requirement type="package" version="3.7.6">python</requirement>
6 </requirements> 7 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
8 python $__tool_directory__/assembly_stats_txt.py 9 python3 $__tool_directory__/assembly_stats_txt.py
9 10
10 '$type' 11 -d '$stats.extra_files_path'
11 '$stats.extra_files_path' 12 -t '$type'
12 '$type' 13 -i '$input'
13 '$bucket' 14 -s '$stats'
14 '$input' 15 -sc '$sortedcontigs'
15 '$stats' 16 -hpng '$histogrampng'
16 '$sortedcontigs' 17 -spng '$summedcontigspng'
17 '$histogrampng' 18 -hd '$histogramdata'
18 '$summedcontigspng' 19 -scd '$summedcontigdata'
19 '$histogramdata' 20
20 '$summedcontigdata' 21 #if $bucket
22 -b
23 #end if
24
21 ]]></command> 25 ]]></command>
22 <inputs> 26 <inputs>
23 <param label="Type of read" name="type" type="select" help="Is this from an genomic (contig) or transcriptomic assembly (isotig) or are these raw reads (read)"> 27 <param label="Type of read" name="type" type="select" help="Is this from an genomic (contig) or transcriptomic assembly (isotig) or are these raw reads (read)">
24 <option value="contig" selected="yes">Contig (if from genomic assembly)</option> 28 <option value="contig" selected="yes">Contig (if from genomic assembly)</option>
25 <option value="isotig">Isotig (if from transcriptomic assembly)</option> 29 <option value="isotig">Isotig (if from transcriptomic assembly)</option>
26 <option value="read">Raw reads from sequencer in FASTA format (useful for 454 data)</option> 30 <option value="read">Raw reads from sequencer in FASTA format (useful for 454 data)</option>
27 </param> 31 </param>
28 <param name="bucket" type="boolean" label="Output histogram with bin sizes=1" truevalue="-b" falsevalue="" help="Use this to specify whether or not bin sizes of 1 should be used when plotting histograms"/> 32 <param name="bucket" type="boolean" label="Output histogram with bin sizes=1" truevalue="true" falsevalue="false" help="Use this to specify whether or not bin sizes of 1 should be used when plotting histograms"/>
29 <param format="fasta" name="input" type="data" label="Source file in FASTA format"/> 33 <param format="fasta" name="input" type="data" label="Source file in FASTA format"/>
30 <param name = "all_outputs" type ="boolean" checked="false" label="Return all output files" help="If checked, all output files will be displayed. If not checked, only the file 'Assembly Statistics' will be provided." /> 34 <param name = "all_outputs" type ="boolean" checked="false" label="Return all output files" help="If checked, all output files will be displayed. If not checked, only the file 'Assembly Statistics' will be provided." />
31 </inputs> 35 </inputs>
32 <outputs> 36 <outputs>
33 <data format="tabular" name="stats" label="Assembly statistics - $input.display_name"/> 37 <data format="tabular" name="stats" label="Assembly statistics - $input.display_name"/>