Mercurial > repos > iuc > seqkit_stats

annotate seqkit_stats.xml @ 6:2cc4745c2cbf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
author iuc
date Sat, 08 Feb 2025 10:46:26 +0000
parents be99273091de
children ef9f258d7439
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a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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1 <tool id="seqkit_stats" name="SeqKit statistics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>of FASTA/Q files</description>
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3 <macros>
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4 <import>macros.xml</import>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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5 </macros>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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6 <expand macro="bio_tools"/>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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7 <expand macro="requirements"/>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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8 <command detect_errors="exit_code"><![CDATA[
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9 #import re
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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10
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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11 #set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier))
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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12 ln -s '${input}' '${input_identifier}' &&
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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13
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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14 seqkit stats
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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15 '${input_identifier}'
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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16 $all
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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17 $basename
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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18 #if str($input.ext) in ['fastqsanger', 'fastqsanger.gz']:
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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19 --fq-encoding sanger
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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20 #end if
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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21 $skip_err
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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22 $tabular
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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23 > '$output'
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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24 ]]></command>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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25 <inputs>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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26 <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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27 <param argument="--all" type="boolean" truevalue="--all" falsevalue="" checked="false" label="Output all statistics?" help="Includes quartiles of seq length, sum_gap, N50"/>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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28 <param argument="--basename" type="boolean" truevalue="--basename" falsevalue="" checked="false" label="Output base name of input file?"/>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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29 <param argument="--skip_err" type="boolean" truevalue="--skip-err" falsevalue="" checked="false" label="Skip errors?" help="Only show warning messages"/>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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30 <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true" label="Output machine-friendly tabular format?"/>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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31 </inputs>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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32 <outputs>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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33 <data name="output" format="txt">
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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34 <change_format>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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35 <when input="tabular" value="--tabular" format="tabular"/>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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36 </change_format>
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37 </data>
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38 </outputs>
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39 <tests>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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40 <test expect_num_outputs="1">
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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41 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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42 <param name="all" value="--all"/>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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43 <output name="output" file="stats_output1.tabular" ftype="tabular"/>
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44 </test>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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45 <test expect_num_outputs="1">
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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46 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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47 <param name="all" value="--all"/>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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48 <output name="output" file="stats_output2.tabular" ftype="tabular"/>
a40d1f17314e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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49 </test>
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50 </tests>
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51 <help>
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52 **What it does**
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53
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54 Outputs simple statistics of FASTA/Q files; number of sequences, sum / min / avg / max sequence lengths, Q1, Q2, Q3,
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55 sum gap, N50, Q20(%), and Q30(%).
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56 </help>
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57 <expand macro="citations"/>
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58 </tool>