Mercurial > repos > devteam > concat

annotate concat.xml @ 4:9a8f22b1a3ed draft

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-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:38:43 -0400
parents 23abefbed3dd
children e24888154cb7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f256537913a1 Imported from capsule None
devteam
parents:
diff changeset
1 <tool id="gops_concat_1" name="Concatenate" version="1.0.1">
4
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
2 <description>two datasets into one dataset</description>
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
3 <macros>
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
4 <import>macros.xml</import>
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
5 </macros>
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
6 <expand macro="requirements" />
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
7 <code file="operation_filter.py"/>
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
8 <command><![CDATA[
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
9 python '$__tool_directory__/gops_concat.py'
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
10 '$input1'
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
11 '$input2'
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
12 '$output'
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
13 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
14 -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
15 $sameformat
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
16 ]]></command>
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
17 <inputs>
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
18 <param name="input1" type="data" format="interval" label="Concatenate" help="First dataset" />
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
19 <param name="input2" type="data" format="interval" label="With" help="Second dataset" />
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
20 <param name="sameformat" type="boolean" truevalue="--sameformat" falsevalue="" checked="true" label="Both datasets are in the same format?" help="If unchecked, Second dataset will be forced into the format of First dataset" />
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
21 </inputs>
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
22 <outputs>
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
23 <data name="output" format_source="input1" metadata_source="input1" />
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
24 </outputs>
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
25 <tests>
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
26 <test>
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
27 <param name="input1" value="1.bed" />
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
28 <param name="input2" value="2.bed" />
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
29 <param name="sameformat" value="true" />
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
30 <output name="output" file="gops_concat_out1.bed" />
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
31 </test>
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
32 <test>
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
33 <param name="input1" value="1.bed" />
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
34 <param name="input2" value="1.interval" />
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
35 <param name="sameformat" value="false" />
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
36 <output name="output" file="gops_concat_out2.bed" />
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
37 </test>
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
38 </tests>
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
39 <help><![CDATA[
0
f256537913a1 Imported from capsule None
devteam
parents:
diff changeset
40 .. class:: infomark
f256537913a1 Imported from capsule None
devteam
parents:
diff changeset
41
f256537913a1 Imported from capsule None
devteam
parents:
diff changeset
42 **TIP:** If your dataset does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.
f256537913a1 Imported from capsule None
devteam
parents:
diff changeset
43
4
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
44 @SCREENCASTS@
0
f256537913a1 Imported from capsule None
devteam
parents:
diff changeset
45
f256537913a1 Imported from capsule None
devteam
parents:
diff changeset
46 **Syntax**
f256537913a1 Imported from capsule None
devteam
parents:
diff changeset
47
f256537913a1 Imported from capsule None
devteam
parents:
diff changeset
48 - **Both datasets are exactly the same filetype** will preserve all extra fields in both files. Leaving this unchecked will force the second dataset to use the same column assignments for chrom, start, end and strand, but will fill extra fields with a period(.). In both cases, the output fields are truncated or padded with fields of periods to maintain a truly tabular output.
f256537913a1 Imported from capsule None
devteam
parents:
diff changeset
49
f256537913a1 Imported from capsule None
devteam
parents:
diff changeset
50 -----
f256537913a1 Imported from capsule None
devteam
parents:
diff changeset
51
f256537913a1 Imported from capsule None
devteam
parents:
diff changeset
52 **Example**
f256537913a1 Imported from capsule None
devteam
parents:
diff changeset
53
1
14cbada56cc0 Added tool image.
devteam <devteam@galaxyproject.org>
parents: 0
diff changeset
54 .. image:: gops_concatenate.gif
4
9a8f22b1a3ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
diff changeset
55 ]]></help>
2
23abefbed3dd planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
56 </tool>