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comparison concat.xml @ 3:32e1c8dac438 draft

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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 18:40:46 -0400
parents 855580142a12
children 35a89f8cc96e
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2:d491589307e7 3:32e1c8dac438
1 <tool id="gops_concat_1" name="Concatenate" version="1.0.1"> 1 <tool id="gops_concat_1" name="Concatenate" version="1.0.1">
2 <description>two datasets into one dataset</description> 2 <description>two datasets into one dataset</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.7.1">bx-python</requirement> 4 <import>macros.xml</import>
5 <requirement type="package" version="1.0.0">galaxy-ops</requirement> 5 </macros>
6 </requirements> 6 <expand macro="requirements" />
7 <command interpreter="python">gops_concat.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} $sameformat</command> 7 <code file="operation_filter.py"/>
8 <inputs> 8 <command><![CDATA[
9 <param format="interval" name="input1" type="data" help="First dataset"> 9 python '$__tool_directory__/gops_concat.py'
10 <label>Concatenate</label> 10 '$input1'
11 </param> 11 '$input2'
12 <param format="interval" name="input2" type="data" help="Second dataset"> 12 '$output'
13 <label>with</label> 13 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
14 </param> 14 -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}
15 <param name="sameformat" type="boolean" truevalue="--sameformat" falsevalue="" label="Both datasets are same filetype?" checked="true" help="If unchecked Second dataset will be forced into format of First dataset"> 15 $sameformat
16 </param> 16 ]]></command>
17 </inputs> 17 <inputs>
18 <outputs> 18 <param name="input1" type="data" format="interval" label="Concatenate" help="First dataset" />
19 <data format="input" name="output" metadata_source="input1" /> 19 <param name="input2" type="data" format="interval" label="With" help="Second dataset" />
20 </outputs> 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" />
21 <code file="operation_filter.py"/> 21 </inputs>
22 <tests> 22 <outputs>
23 <test> 23 <data name="output" format_source="input1" metadata_source="input1" />
24 <param name="input1" value="1.bed" /> 24 </outputs>
25 <param name="input2" value="2.bed" /> 25 <tests>
26 <param name="sameformat" value="true" /> 26 <test>
27 <output name="output" file="gops_concat_out1.bed" /> 27 <param name="input1" value="1.bed" />
28 </test> 28 <param name="input2" value="2.bed" />
29 <test> 29 <param name="sameformat" value="true" />
30 <param name="input1" value="1.bed" /> 30 <output name="output" file="gops_concat_out1.bed" />
31 <param name="input2" value="1.interval" /> 31 </test>
32 <param name="sameformat" value="false" /> 32 <test>
33 <output name="output" file="gops_concat_out2.bed" /> 33 <param name="input1" value="1.bed" />
34 </test> 34 <param name="input2" value="1.interval" />
35 </tests> 35 <param name="sameformat" value="false" />
36 <help> 36 <output name="output" file="gops_concat_out2.bed" />
37 37 </test>
38 </tests>
39 <help><![CDATA[
38 .. class:: infomark 40 .. class:: infomark
39 41
40 **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. 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.
41 43
42 ----- 44 @SCREENCASTS@
43
44 **Screencasts!**
45
46 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
47
48 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
49
50 -----
51 45
52 **Syntax** 46 **Syntax**
53 47
54 - **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. 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.
55 49
56 ----- 50 -----
57 51
58 **Example** 52 **Example**
59 53
60 .. image:: gops_concatenate.gif 54 .. image:: gops_concatenate.gif
61 55 ]]></help>
62 </help>
63 </tool> 56 </tool>