Mercurial > repos > mvdbeek > bam_readtagger

annotate filter_insertions.xml @ 41:4fdf606153df draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 89e57ebe9ad1eb4ba44167f83935869fb54b8396-dirty
author mvdbeek
date Thu, 24 May 2018 11:05:38 -0400
parents 4b1ebfcd0f46
children 5b8781514bc1
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mvdbeek
parents: 40
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1 <tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.11">
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2 <description>based on softclips in control files</description>
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mvdbeek
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3 <requirements>
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mvdbeek
parents: 40
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4 <requirement type="package" version="0.4.11">readtagger</requirement>
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mvdbeek
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5 </requirements>
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mvdbeek
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6 <version_command>confirm_insertions --version</version_command>
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7 <command detect_errors="aggressive"><![CDATA[
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mvdbeek
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8 ln -fs $putative_insertions putative_insertions.gff &&
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mvdbeek
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9 ln -fs $all_insertions all_insertions.gff &&
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10 ln -fs $all_controls all_controls_path.gff &&
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11 confirm_insertions
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mvdbeek
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12 --putative_insertions_path putative_insertions.gff
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mvdbeek
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13 --all_treatments_path all_insertions.gff
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mvdbeek
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14 #for p in $all_controls
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15 --all_controls_paths '$p'
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16 #end for
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17 --output_path '$output'
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18 $output_discard
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19 ]]></command>
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mvdbeek
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20 <inputs>
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21 <param name="putative_insertions" label="Path to filtered putative insertinos" argument="--putative_insertions_path" type="data" format="gff3"/>
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22 <param name="all_insertions" label="Path to all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/>
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23 <param name="all_controls" label="Path to all unfiltered insertions from one or more control samples" argument="--all_controls_path" multiple="True" type="data" format="gff3"/>
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24 <param name="output_discard" label="Output discarded records? Discarded records will be marked as failed." truevalue="--output_discarded_records" falsevalue="--no_output_discarded_records" checked="True" type="boolean"/>
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25 </inputs>
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26 <outputs>
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27 <data name="output" format="gff3"/>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="putative_insertions" value="putative_insertions.gff" ftype="gff3"/>
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32 <param name="all_insertions" value="all_treatment_insertions.gff" ftype="gff3"/>
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33 <param name="all_controls" value="all_control_insertions.gff" ftype="gff3"/>
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34 <output name="output" file="confirmed_insertions.gff" ftype="gff3"/>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 .. code-block::
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41 Usage: confirm_insertions [OPTIONS]
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43 Confirm insertions by checking that control file does not contain the same
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44 clipping pattern.
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46 Options:
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47 -p, --putative_insertions_path PATH
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48 Path to file containing putative somatic
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49 insertions [required]
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50 -t, --all_treatments_path PATH Path to file containing all treatment
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51 insertions [required]
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52 -c, --all_controls_path PATH Path to file containing all control
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53 insertions [required]
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54 -o, --output_path TEXT Write annotated output to this Path.
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55 --output_discarded_records / --no_output_discarded_records
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56 Discard an alternative flag if the current
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57 read is in a proper pair.
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58 --version Show the version and exit.
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59 --help Show this message and exit.
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60 ]]></help>
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61 </tool>