Mercurial > repos > mvdbeek > bam_readtagger

annotate filter_insertions.xml @ 39:432bb619c079 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 5adc383da0811cbfc6f82c6bad594efbe6c7b682-dirty
author mvdbeek
date Thu, 15 Mar 2018 07:20:58 -0400
parents f6311a04a6c9
children 4b1ebfcd0f46
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mvdbeek
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1 <tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.9">
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mvdbeek
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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
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4 <requirement type="package" version="0.4.9">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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mvdbeek
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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 &&
432bb619c079 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 5adc383da0811cbfc6f82c6bad594efbe6c7b682-dirty
mvdbeek
parents: 38
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9 ln -fs $all_insertions all_insertions.gff &&
432bb619c079 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 5adc383da0811cbfc6f82c6bad594efbe6c7b682-dirty
mvdbeek
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10 ln -fs $all_controls all_controls_path.gff &&
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mvdbeek
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11 confirm_insertions
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432bb619c079 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 5adc383da0811cbfc6f82c6bad594efbe6c7b682-dirty
mvdbeek
parents: 38
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12 --putative_insertions_path putative_insertions.gff
432bb619c079 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 5adc383da0811cbfc6f82c6bad594efbe6c7b682-dirty
mvdbeek
parents: 38
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13 --all_treatments_path all_insertions.gff
432bb619c079 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 5adc383da0811cbfc6f82c6bad594efbe6c7b682-dirty
mvdbeek
parents: 38
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14 --all_controls_path all_controls_path.gff
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mvdbeek
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15 --output_path '$output'
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mvdbeek
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16 $output_discard
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mvdbeek
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17 ]]></command>
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mvdbeek
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18 <inputs>
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mvdbeek
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19 <param name="putative_insertions" label="Path to filtered putative insertinos" argument="--putative_insertions_path" type="data" format="gff3"/>
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mvdbeek
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20 <param name="all_insertions" label="Path to all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/>
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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21 <param name="all_controls" label="Path to all unfiltered insertions from control sample" argument="--all_controls_path" type="data" format="gff3"/>
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mvdbeek
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22 <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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mvdbeek
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23 </inputs>
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mvdbeek
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24 <outputs>
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25 <data name="output" format="gff3"/>
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mvdbeek
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26 </outputs>
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mvdbeek
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27 <tests>
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mvdbeek
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28 <test>
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mvdbeek
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29 <param name="putative_insertions" value="putative_insertions.gff" ftype="gff3"/>
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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30 <param name="all_insertions" value="all_treatment_insertions.gff" ftype="gff3"/>
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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31 <param name="all_controls" value="all_control_insertions.gff" ftype="gff3"/>
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mvdbeek
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32 <output name="output" file="confirmed_insertions.gff" ftype="gff3"/>
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mvdbeek
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33 </test>
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34 </tests>
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35 <help><![CDATA[
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mvdbeek
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36 .. code-block::
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39 Usage: confirm_insertions [OPTIONS]
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40
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41 Confirm insertions by checking that control file does not contain the same
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42 clipping pattern.
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43
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44 Options:
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45 -p, --putative_insertions_path PATH
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46 Path to file containing putative somatic
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47 insertions [required]
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mvdbeek
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48 -t, --all_treatments_path PATH Path to file containing all treatment
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49 insertions [required]
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mvdbeek
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50 -c, --all_controls_path PATH Path to file containing all control
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mvdbeek
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51 insertions [required]
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mvdbeek
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52 -o, --output_path TEXT Write annotated output to this Path.
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mvdbeek
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53 --output_discarded_records / --no_output_discarded_records
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mvdbeek
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54 Discard an alternative flag if the current
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mvdbeek
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55 read is in a proper pair.
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mvdbeek
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56 --version Show the version and exit.
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mvdbeek
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57 --help Show this message and exit.
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58 ]]></help>
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59 </tool>