Mercurial > repos > iuc > presto_partition

annotate presto_partition.xml @ 1:c3bf9c466305 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit a42c43c1528ae7b7efe2c5ef848681d574df0405"
author iuc
date Tue, 22 Jun 2021 16:33:38 +0000
parents 0b103d43a2c7
children 824d24bfe8dd
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0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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1 <tool id="presto_partition" name="pRESTO Partition" version="@PRESTO_VERSION@">
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2 <description>Partition a file in two</description>
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0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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4 <macros>
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5 <import>presto_macros.xml</import>
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6 </macros>
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0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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8 <expand macro="requirements"/>
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10 <version_command>SplitSeq.py --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ln -s '$fastq_in' in.fastq &&
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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13 SplitSeq.py group
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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14 -s in.fastq
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15 -f '$field'
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16 --num '$threshold'
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17 --outname=tmp_group &&
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18 mv './tmp_group_under-${threshold}.fastq' '$lower_out' &&
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19 mv './tmp_group_atleast-${threshold}.fastq' '$upper_out'
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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20 ]]></command>
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22 <inputs>
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23 <param argument="-s" name="fastq_in" type="data" format="fastq" label="Input FASTQ file" help="FASTQ file of sequences with barcodes/UMIs in an annotation."/>
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24 <param argument="-f" name="field" type="text" value="" label="Annotation Field" help="Name of the numeric annotation field to partition by."/>
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25 <param argument="--num" name="threshold" type="integer" value="0" label="Threshold" help="Numeric threshold. File will be partitions be into n &lt; threshold and n &gt;= threshold."/>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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26 </inputs>
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28 <outputs>
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29 <data name="lower_out" format="fastq" label="Sequences with $field &lt; $threshold"/>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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30 <data name="upper_out" format="fastq" label="Sequences with $field &gt;= $threshold"/>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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31 </outputs>
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33 <tests>
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34 <test>
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35 <param name="fastq_in" value="presto_splitseq_partition_test_in.fastq"/>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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36 <param name="field" value="CONSCOUNT"/>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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37 <param name="threshold" value="3"/>
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38 <output name="lower_out" file="presto_splitseq_partition_test_out_under.fastq" sort="true"/>
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39 <output name="upper_out" file="presto_splitseq_partition_test_out_atleast.fastq" sort="true"/>
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40 </test>
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41 </tests>
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43 <help><![CDATA[
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44 Uses pRESTO SplitSeq.py group to partition a file of sequences into two files. The input file is split based on a numeric
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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45 annotation field to yield one file which contains all sequences with the field value less than the provided threshold and
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46 a second file with all sequences with the field value greater than or equal to the threshold.
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47
1
c3bf9c466305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit a42c43c1528ae7b7efe2c5ef848681d574df0405"
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48 See the `pRESTO online help <@PRESTO_BASE_URL@/en/stable>`_ for more information.
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50 @HELP_NOTE@
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51 ]]></help>
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52 <expand macro="citations" />
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53 </tool>