Mercurial > repos > iuc > presto_partition

annotate presto_partition.xml @ 4:1f3ae16f3655 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 1beb51cefbe9e6edc8930c7ae0421f28e7bb93c8
author iuc
date Fri, 04 Oct 2024 09:05:58 +0000
parents 620f3b0a1430
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
620f3b0a1430 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"
iuc
parents: 2
diff changeset
1 <tool id="presto_partition" name="pRESTO Partition" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
2 <description>Partition a file in two</description>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
3 <macros>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
4 <import>presto_macros.xml</import>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
5 </macros>
4
1f3ae16f3655 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 1beb51cefbe9e6edc8930c7ae0421f28e7bb93c8
iuc
parents: 3
diff changeset
6 <expand macro="bio_tools"/>
0
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
7
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
8 <expand macro="requirements"/>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
9
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
10 <version_command>SplitSeq.py --version</version_command>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
12 ln -s '$fastq_in' in.fastq &&
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
13 SplitSeq.py group
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
14 -s in.fastq
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
15 -f '$field'
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
16 --num '$threshold'
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
17 --outname=tmp_group &&
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
18 mv './tmp_group_under-${threshold}.fastq' '$lower_out' &&
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
19 mv './tmp_group_atleast-${threshold}.fastq' '$upper_out'
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
20 ]]></command>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
21
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
22 <inputs>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
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."/>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
24 <param argument="-f" name="field" type="text" value="" label="Annotation Field" help="Name of the numeric annotation field to partition by."/>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
26 </inputs>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
27
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
28 <outputs>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
31 </outputs>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
32
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
33 <tests>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
34 <test>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
36 <param name="field" value="CONSCOUNT"/>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
37 <param name="threshold" value="3"/>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
38 <output name="lower_out" file="presto_splitseq_partition_test_out_under.fastq" sort="true"/>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
39 <output name="upper_out" file="presto_splitseq_partition_test_out_atleast.fastq" sort="true"/>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
40 </test>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
41 </tests>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
42
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
43 <help><![CDATA[
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
45 annotation field to yield one file which contains all sequences with the field value less than the provided threshold and
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
46 a second file with all sequences with the field value greater than or equal to the threshold.
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
47
1
c3bf9c466305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit a42c43c1528ae7b7efe2c5ef848681d574df0405"
iuc
parents: 0
diff changeset
48 See the `pRESTO online help <@PRESTO_BASE_URL@/en/stable>`_ for more information.
0
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
49
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
50 @HELP_NOTE@
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
51 ]]></help>
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
52 <expand macro="citations" />
0b103d43a2c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
53 </tool>