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annotate 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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1 <tool id="gops_concat_1" name="Concatenate" version="1.0.1">
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2 <description>two datasets into one dataset</description>
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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" />
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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" />
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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" />
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31 </test>
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32 <test>
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33 <param name="input1" value="1.bed" />
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34 <param name="input2" value="1.interval" />
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35 <param name="sameformat" value="false" />
32e1c8dac438 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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36 <output name="output" file="gops_concat_out2.bed" />
32e1c8dac438 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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37 </test>
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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>