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annotate concat.xml @ 4:35a89f8cc96e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit 58cb53d87440bd45e014fb37cddc276dc79b9d94
author devteam
date Mon, 25 Jun 2018 19:48:09 -0400
parents 32e1c8dac438
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1 <tool id="gops_concat_1" name="Concatenate" version="1.0.1">
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2 <description>two BED files</description>
3
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <code file="operation_filter.py"/>
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8 <command><![CDATA[
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9 python '$__tool_directory__/gops_concat.py'
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10 '$input1'
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11 '$input2'
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12 '$output'
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13 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
32e1c8dac438 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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14 -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}
32e1c8dac438 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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15 $sameformat
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16 ]]></command>
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17 <inputs>
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18 <param name="input1" type="data" format="interval" label="Concatenate" help="First dataset" />
32e1c8dac438 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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19 <param name="input2" type="data" format="interval" label="With" help="Second dataset" />
32e1c8dac438 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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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" />
32e1c8dac438 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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21 </inputs>
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22 <outputs>
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23 <data name="output" format_source="input1" metadata_source="input1" />
32e1c8dac438 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="input1" value="1.bed" />
32e1c8dac438 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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28 <param name="input2" value="2.bed" />
32e1c8dac438 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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29 <param name="sameformat" value="true" />
32e1c8dac438 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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30 <output name="output" file="gops_concat_out1.bed" />
32e1c8dac438 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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31 </test>
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32 <test>
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33 <param name="input1" value="1.bed" />
32e1c8dac438 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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34 <param name="input2" value="1.interval" />
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35 <param name="sameformat" value="false" />
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36 <output name="output" file="gops_concat_out2.bed" />
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37 </test>
32e1c8dac438 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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38 </tests>
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39 <help><![CDATA[
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40 .. class:: infomark
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41
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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.
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43
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44 @SCREENCASTS@
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45
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46 **Syntax**
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47
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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.
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49
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50 -----
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51
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52 **Example**
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53
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54 .. image:: gops_concatenate.gif
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55 ]]></help>
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56 </tool>