Mercurial > repos > iuc > circos

annotate tiles-from-interval.xml @ 12:290a11559985 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit e3d1aad2204a3385aa66f3b0625747151e9f94e8"
author iuc
date Mon, 22 Nov 2021 12:23:12 +0000
parents 31a35811dda6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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"?>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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2 <tool id="circos_interval_to_tile" name="Circos: Interval to Tiles" version="@WRAPPER_VERSION@">
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3 <description>reformats interval files to prepare for Circos tile plots</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
9
df7356989ac1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 041a4d1618298f540e3917f00781e09ec7d71b75"
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7 <edam_topics>
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8 <edam_topic>topic_0797</edam_topic>
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9 <edam_topic>topic_0092</edam_topic>
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10 </edam_topics>
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11 <edam_operations>
df7356989ac1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 041a4d1618298f540e3917f00781e09ec7d71b75"
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12 <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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13 </edam_operations>
11
31a35811dda6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit b9ec351920dbc83fa14bd1f8cfdd0a6a19b89473"
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14 <expand macro="requirements" />
2
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15 <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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16 python
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17 #if $ref.ref_source == 'gff3':
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18 '$__tool_directory__/tiles-from-gff3.py' '$input' '${ref.attr}'
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19 #else
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20 '$__tool_directory__/tiles-from-bed.py' '$input'
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21 #end if
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22 > '$output'
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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23 ]]></command>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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24 <inputs>
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25 <conditional name="ref">
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26 <param name="ref_source" type="select" label="Data Format">
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27 <option value="bed" selected="true">BED6+</option>
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28 <option value="gff3">GFF3</option>
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29 </param>
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30 <when value="bed">
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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31 <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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32 </when>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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33 <when value="gff3">
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34 <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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35 <param name="attr" type="text" label="GFF3 Attribute to pull value from" />
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36 </when>
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37 </conditional>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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38 </inputs>
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39 <outputs>
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40 <data name="output" format="tabular" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 <conditional name="ref">
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45 <param name="ref_source" value="bed" />
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46 <param name="input" value="tiles/1.bed" ftype="bed" />
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47 </conditional>
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48 <output name="output" file="tiles/1.out" ftype="tabular" />
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49 </test>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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50 <test>
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51 <conditional name="ref">
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52 <param name="ref_source" value="gff3" />
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53 <param name="input" value="tiles/2.gff3" ftype="gff3" />
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54 <param name="attr" value="Name" />
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55 </conditional>
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56 <output name="output" file="tiles/2.out" ftype="tabular" />
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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60 Converts standard BED3+ and GFF3 files into a format appropriate for Circos data tracks, especially tile tracks.
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61
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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62 BED3 files do not need conversion, Circos can accept these files directly.
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63 ]]></help>
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64 <expand macro="citations" />
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65 </tool>