Mercurial > repos > iuc > pretext_graph

annotate pretext_graph.xml @ 2:b3c4bad4b615 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext commit f58b497b52f86a3d1c2c5eedbdf684145d43f1e8
author iuc
date Fri, 07 Nov 2025 16:40:03 +0000
parents 204c10e3703c
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716ec61855a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit e387e8541eb3e9c5ce56440f955a3b6f2aa27d08
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1 <tool id="pretext_graph" name="Pretextgraph" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>Embed bedgraph formatted data inside a Pretext contact map.</description>
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3 <macros>
2
b3c4bad4b615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext commit f58b497b52f86a3d1c2c5eedbdf684145d43f1e8
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4 <token name="@TOOL_VERSION@">0.0.9</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">pretextgraph</requirement>
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9 <requirement type="package" version="377"> ucsc-bigwigtobedgraph</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
716ec61855a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit e387e8541eb3e9c5ce56440f955a3b6f2aa27d08
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12 cp '$pretext' input.pretext &&
716ec61855a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit e387e8541eb3e9c5ce56440f955a3b6f2aa27d08
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13 #if $input.is_of_type("bedgraph"):
716ec61855a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit e387e8541eb3e9c5ce56440f955a3b6f2aa27d08
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14 cat '$input' |
716ec61855a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit e387e8541eb3e9c5ce56440f955a3b6f2aa27d08
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15 #else if $input.is_of_type("bigwig"):
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16 ln -s '$input' input.bigwig &&
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17 bigWigToBedGraph input.bigwig /dev/stdout |
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18 #end if
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19 PretextGraph -i input.pretext
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20 #if $name:
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21 -n '$name'
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22 #end if
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23 -o output.pretext
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24 ]]></command>
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25 <inputs>
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26 <param name="input" type="data" format="bigwig,bedgraph" label="Input bigwig or bedgraph file"/>
716ec61855a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit e387e8541eb3e9c5ce56440f955a3b6f2aa27d08
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27 <param name="pretext" type="data" format="pretext" label="Pretext file" help="Sequence names in the Pretext file must match sequence names in the bedgraph data; although relative sort order is unimportant."/>
716ec61855a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit e387e8541eb3e9c5ce56440f955a3b6f2aa27d08
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28 <param name="name" type="text" label="Label for the graph" optional="true"/>
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29 </inputs>
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30 <outputs>
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31 <data name="graph_out" format="pretext" from_work_dir="output.pretext" label="${tool.name} on ${on_string}"/>
716ec61855a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit e387e8541eb3e9c5ce56440f955a3b6f2aa27d08
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32 </outputs>
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33 <tests>
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34 <!-- BIGWIG TEST -->
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35 <test expect_num_outputs="1">
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36 <param name="input" value="input_graph.bw" ftype="bigwig"/>
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37 <param name="pretext" value="input_graph.pretext" ftype="pretext"/>
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38 <param name="name" value="testing"/>
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39 <output name="graph_out" file="output_4.pretext"/>
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40 </test>
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41 <!-- BEDGRAPH TEST -->
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42 <test expect_num_outputs="1">
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43 <param name="input" value="input_graph.bgr" ftype="bedgraph"/>
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44 <param name="pretext" value="input_graph.pretext" ftype="pretext"/>
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45 <param name="name" value="testing_2"/>
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46 <output name="graph_out" file="output_5.pretext"/>
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47 </test>
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48 </tests>
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49 <help><![CDATA[
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50 Adds additional data onto existing pretextmap files.
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51 Input Pretext file acts as a foundation for additional data to be added onto.
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52 Sequence names in the Pretext file must match sequence names in the bedgraph data; although relative sort order is unimportant.
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53 The chosen name acts as a lable on the graph.
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54 ]]></help>
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55 <citations>
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56 <citation type="bibtex">
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57 @misc{Harry_et_al,
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58 Author={Harry, E},
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59 title={Paired REad TEXTure Graph: Embeds bedgraph data into Pretext contact maps.},
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60 url = {https://github.com/wtsi-hpag/PretextGraph},}
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61 </citation>
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62 </citations>
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63 </tool>