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annotate text-from-interval.xml @ 10:7f13dc906cb9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 164c36ba98fe4cd293e035efca00a9efa885a7ec"
author iuc
date Mon, 11 Oct 2021 10:09:51 +0000
parents df7356989ac1
children 31a35811dda6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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1 <?xml version="1.0"?>
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2 <tool id="circos_interval_to_text" name="Circos: Interval to Circos Text Labels" version="@WRAPPER_VERSION@">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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3 <description>reformats interval files to prepare for Circos text labels</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements">
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8 </expand>
9
df7356989ac1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 041a4d1618298f540e3917f00781e09ec7d71b75"
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9 <edam_topics>
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10 <edam_topic>topic_0797</edam_topic>
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11 <edam_topic>topic_0092</edam_topic>
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12 </edam_topics>
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13 <edam_operations>
df7356989ac1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 041a4d1618298f540e3917f00781e09ec7d71b75"
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14 <edam_operation>operation_3434</edam_operation>
df7356989ac1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 041a4d1618298f540e3917f00781e09ec7d71b75"
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15 </edam_operations>
2
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16 <command detect_errors="exit_code"><![CDATA[
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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17 python
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18 #if $ref.ref_source == 'gff3':
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19 '$__tool_directory__/text-from-gff3.py' '$input' '${ref.attr}'
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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20 #else
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21 '$__tool_directory__/text-from-bed.py' '$input'
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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22 #end if
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23 > '$output'
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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24 ]]></command>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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25 <inputs>
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26 <conditional name="ref">
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27 <param name="ref_source" type="select" label="Data Format">
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28 <option value="bed" selected="true">BED6+</option>
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29 <option value="gff3">GFF3</option>
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30 </param>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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31 <when value="bed">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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32 <param name="input" type="data" format="bed" label="BED File (BED6+ only)" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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33 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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34 <when value="gff3">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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35 <param name="input" type="data" format="gff3" label="GFF3 File" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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36 <param name="attr" type="text" label="GFF3 Attribute to pull value from" />
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37 </when>
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38 </conditional>
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39 </inputs>
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40 <outputs>
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41 <data name="output" format="tabular" />
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42 </outputs>
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43 <tests>
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44 <test>
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45 <conditional name="ref">
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46 <param name="ref_source" value="bed" />
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47 <param name="input" value="text/1.bed" ftype="bed" />
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48 </conditional>
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49 <output name="output" file="text/1.out" ftype="tabular" />
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50 </test>
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51 <test>
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52 <conditional name="ref">
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53 <param name="ref_source" value="gff3" />
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54 <param name="input" value="text/2.gff3" ftype="gff3" />
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55 <param name="attr" value="Name" />
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56 </conditional>
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57 <output name="output" file="text/2.out" ftype="tabular" />
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61 Converts standard BED6+ and GFF3 files into a format appropriate for Circos data tracks, especially text tracks.
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62
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63 BED3 files cannot be used as they lack the name field.
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64 ]]></help>
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65 <expand macro="citations" />
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66 </tool>