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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
author artbio
date Wed, 13 Dec 2023 00:20:07 +0000
parents 32b19379cd25
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
artbio
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1 <tool id="justgzip" name="Gzip datasets" version="2.8+galaxy0" profile="21.01">
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401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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2 <description></description>
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285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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4 <requirements>
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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5 <requirement type="package" version="2.8">pigz</requirement>
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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6 </requirements>
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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7
0
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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8 <stdio>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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9 <exit_code range="1:" level="fatal" description="Tool exception" />
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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10 </stdio>
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285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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12 <command detect_errors="exit_code"><![CDATA[
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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13 pigz --processes \${GALAXY_SLOTS:-4} -c '${input1}' > '$output'
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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14 #if ($input1.ext.startswith("fastq") and not $input1.ext.endswith(".gz")) or $input1.ext in ["fasta", "paf", "gff3", "nii1", "nii2", "gii", "tabular"]:
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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15 #set ext = $input1.ext + ".gz"
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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16 #else
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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17 #set ext = "gz"
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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18 #end if
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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19 && echo '{"output": {"ext": "$ext"}}' >> galaxy.json
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401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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20 ]]></command>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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21 <inputs>
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285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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22 <param format="data" name="input1" type="data" label="Input file" help="file to compress" />
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401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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23 </inputs>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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24 <outputs>
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285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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25 <data name="output" format="auto" label="${input1.name}.gz" />
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401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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26 </outputs>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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27 <tests>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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28 <test>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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29 <param name="input1" value="file1" ftype="fastq" />
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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30 <output name="output" file="file1.gz" decompress="True" ftype="fastq.gz"/>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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31 </test>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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32 <test>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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33 <param name="input1" value="file1" ftype="fastqsanger" />
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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34 <output name="output" file="file1.gz" decompress="True" ftype="fastqsanger.gz" />
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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35 </test>
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285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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36 </tests>
0
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401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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38 <help>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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40 .. class:: infomark
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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42 **What it does**
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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2
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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44 Just **gzip** datasets, but does it faster with the multithreaded pigz program !
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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46 Accepted input formats include:
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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47 - fastq
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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48 - fastqsanger
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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49 - fasta
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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50 - paf
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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51 - gff3
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52 - nii1
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53 - nii2
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54 - gii
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55 - tabular
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56 - txt
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57 - ...
285d48249ba2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
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58
0
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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59 </help>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
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60 </tool>
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