Mercurial > repos > mvdbeek > bam_readtagger

annotate filter_insertions.xml @ 78:6178c24ddd5a draft

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"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
author mvdbeek
date Tue, 07 Apr 2020 08:57:47 -0400
parents 8c3d8d38674a
children c42dd2551c9c
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1 <tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.24">
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2 <description>based on softclips in control files</description>
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3 <requirements>
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4 <requirement type="package" version="0.5.24">readtagger</requirement>
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5 </requirements>
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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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8 ln -fs $putative_insertions putative_insertions.gff &&
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9 ln -fs $all_insertions all_insertions.gff &&
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10 #for i, p in enumerate($all_controls)
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11 ln -fs '$p' all_controls_${i}.gff &&
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12 #end for
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13 confirm_insertions
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14 --putative_insertions_path putative_insertions.gff
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15 --all_treatments_path all_insertions.gff
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16 #for i, p in enumerate($all_controls)
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17 --all_controls_paths all_controls_${i}.gff
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18 #end for
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19 --output_path '$output'
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20 $output_discard
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21 --min_length $min_length
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22 ]]></command>
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23 <inputs>
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24 <param name="putative_insertions" label="Select dataset with filtered putative insertions" argument="--putative_insertions_path" type="data" format="gff3"/>
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25 <param name="all_insertions" label="Select datasets with all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/>
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26 <param name="all_controls" label="Select datasets with all unfiltered insertions from one or more control samples" argument="--all_controls_path" multiple="True" type="data" format="gff3"/>
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27 <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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28 <param argument="--min_length" label="Minimum length necessary to match clip patterns" help="If too low will create false matches, if too high will not find legitimate matches." value="4" min="1" type="integer"/>
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29 </inputs>
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30 <outputs>
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31 <data name="output" format="gff3"/>
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="putative_insertions" value="putative_insertions.gff" ftype="gff3"/>
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36 <param name="all_insertions" value="all_treatment_insertions.gff" ftype="gff3"/>
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37 <param name="all_controls" value="all_control_insertions.gff" ftype="gff3"/>
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38 <output name="output" file="confirmed_insertions.gff" ftype="gff3"/>
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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42 .. code-block::
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45 Usage: confirm_insertions [OPTIONS]
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47 Confirm insertions by checking that control file does not contain the same
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48 clipping pattern.
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50 Options:
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51 -p, --putative_insertions_path PATH
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52 Path to file containing putative somatic
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53 insertions [required]
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54 -t, --all_treatments_path PATH Path to file containing all treatment
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55 insertions [required]
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56 -c, --all_controls_path PATH Path to file containing all control
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57 insertions [required]
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58 -o, --output_path TEXT Write annotated output to this Path.
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59 --output_discarded_records / --no_output_discarded_records
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60 Discard an alternative flag if the current
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61 read is in a proper pair.
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62 --version Show the version and exit.
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63 --help Show this message and exit.
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64 ]]></help>
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65 </tool>