Mercurial > repos > mvdbeek > bam_readtagger
annotate filter_insertions.xml @ 51:08656cd6c989 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 459f27d06d9541ec2aa2812278e63502bd3185d2
author | mvdbeek |
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date | Fri, 15 Feb 2019 02:31:18 -0500 |
parents | f4344d943248 |
children | b03c6d8c37c1 |
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51
08656cd6c989
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 459f27d06d9541ec2aa2812278e63502bd3185d2
mvdbeek
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1 <tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.19"> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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2 <description>based on softclips in control files</description> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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3 <requirements> |
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08656cd6c989
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 459f27d06d9541ec2aa2812278e63502bd3185d2
mvdbeek
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4 <requirement type="package" version="0.4.19">readtagger</requirement> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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5 </requirements> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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6 <version_command>confirm_insertions --version</version_command> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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7 <command detect_errors="aggressive"><![CDATA[ |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 5adc383da0811cbfc6f82c6bad594efbe6c7b682-dirty
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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
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9 ln -fs $all_insertions all_insertions.gff && |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 63220935ba51b0b5480da88017d58616bf671337-dirty
mvdbeek
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10 #for i, p in enumerate($all_controls) |
5b8781514bc1
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 63220935ba51b0b5480da88017d58616bf671337-dirty
mvdbeek
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11 ln -fs '$p' all_controls_${i}.gff && |
5b8781514bc1
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 63220935ba51b0b5480da88017d58616bf671337-dirty
mvdbeek
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12 #end for |
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f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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13 confirm_insertions |
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432bb619c079
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 5adc383da0811cbfc6f82c6bad594efbe6c7b682-dirty
mvdbeek
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14 --putative_insertions_path putative_insertions.gff |
432bb619c079
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 5adc383da0811cbfc6f82c6bad594efbe6c7b682-dirty
mvdbeek
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15 --all_treatments_path all_insertions.gff |
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5b8781514bc1
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 63220935ba51b0b5480da88017d58616bf671337-dirty
mvdbeek
parents:
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16 #for i, p in enumerate($all_controls) |
5b8781514bc1
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 63220935ba51b0b5480da88017d58616bf671337-dirty
mvdbeek
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17 --all_controls_paths all_controls_${i}.gff |
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4fdf606153df
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 89e57ebe9ad1eb4ba44167f83935869fb54b8396-dirty
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18 #end for |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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19 --output_path '$output' |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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20 $output_discard |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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21 ]]></command> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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22 <inputs> |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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23 <param name="putative_insertions" label="Path to filtered putative insertinos" argument="--putative_insertions_path" type="data" format="gff3"/> |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
parents:
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24 <param name="all_insertions" label="Path to all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/> |
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4fdf606153df
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 89e57ebe9ad1eb4ba44167f83935869fb54b8396-dirty
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25 <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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432bb619c079
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 5adc383da0811cbfc6f82c6bad594efbe6c7b682-dirty
mvdbeek
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26 <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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f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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27 </inputs> |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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28 <outputs> |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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29 <data name="output" format="gff3"/> |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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30 </outputs> |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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31 <tests> |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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32 <test> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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33 <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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34 <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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35 <param name="all_controls" value="all_control_insertions.gff" ftype="gff3"/> |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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36 <output name="output" file="confirmed_insertions.gff" ftype="gff3"/> |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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37 </test> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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38 </tests> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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39 <help><![CDATA[ |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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40 .. code-block:: |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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41 |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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42 |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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43 Usage: confirm_insertions [OPTIONS] |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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44 |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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45 Confirm insertions by checking that control file does not contain the same |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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46 clipping pattern. |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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47 |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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48 Options: |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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49 -p, --putative_insertions_path PATH |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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50 Path to file containing putative somatic |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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51 insertions [required] |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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52 -t, --all_treatments_path PATH Path to file containing all treatment |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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53 insertions [required] |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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54 -c, --all_controls_path PATH Path to file containing all control |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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55 insertions [required] |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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56 -o, --output_path TEXT Write annotated output to this Path. |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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57 --output_discarded_records / --no_output_discarded_records |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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58 Discard an alternative flag if the current |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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59 read is in a proper pair. |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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60 --version Show the version and exit. |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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61 --help Show this message and exit. |
f6311a04a6c9
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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62 ]]></help> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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63 </tool> |