Mercurial > repos > erasmus-medical-center > dr_disco
annotate dr-disco_classify.xml @ 11:3743fd602fa9 draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 183cebdfe3a34204fd8aa1c6dce6bf6514b94c2d
author | erasmus-medical-center |
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date | Fri, 03 Nov 2017 07:23:57 -0400 |
parents | f2c70d589596 |
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rev | line source |
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922b52cf9b35
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b4991fb40364a975d0ea782035b930874c57665c
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1 <tool id="dr_disco_classify" name="Dr. Disco (classify)" version="@TOOL_VERSION@"> |
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5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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2 <description>Classifies detected break-points in RNA-seq based on corresponding statistics and blacklists</description> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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3 |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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4 <macros> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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5 <import>macros.xml</import> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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6 </macros> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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7 |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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8 <expand macro="requirements"/> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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9 <expand macro="version_command"/> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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10 |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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11 <command detect_errors="exit_code"><![CDATA[ |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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12 dr-disco |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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13 classify |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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14 |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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15 ${only_valid} |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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16 |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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17 #if $blacklist_regions: |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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18 --blacklist-regions '${blacklist_regions}' |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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19 #end if |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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20 |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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21 #if $blacklist_junctions: |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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22 --blacklist-junctions '${blacklist_junctions}' |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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23 #end if |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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24 |
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f2c70d589596
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 3b03a60c8a46cc23f6fbbb9e32111b39c6044fad
erasmus-medical-center
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25 --min-chim-overhang '${min_chim_overhang}' |
f2c70d589596
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 3b03a60c8a46cc23f6fbbb9e32111b39c6044fad
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26 |
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5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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27 '${dr_disco_detect_output}' |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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28 '${dr_disco_classify_output}' |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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29 ]]></command> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
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30 |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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31 <inputs> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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32 <param name="dr_disco_detect_output" type="data" format="tabular" label="Output of Dr. Disco Detect" /> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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33 <param name="only_valid" argument="--only-valid" truevalue="--only-valid" falsevalue="" type="boolean" /> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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34 |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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35 <param name="blacklist_regions" argument="--blacklist-regions" type="data" format="bed" optional="True" label="Blacklist Regions" help="List of regions known to be false positives (https://github.com/yhoogstrate/dr-disco/tree/master/share/)" /> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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36 <param name="blacklist_junctions" argument="--blacklist-junctions" type="data" format="tabular" optional="True" label="Blacklist Junctions" help="List of junctions know to be false positives (https://github.com/yhoogstrate/dr-disco/tree/master/share/)" /> |
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f2c70d589596
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 3b03a60c8a46cc23f6fbbb9e32111b39c6044fad
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37 |
f2c70d589596
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 3b03a60c8a46cc23f6fbbb9e32111b39c6044fad
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38 <param name="min_chim_overhang" type="integer" min="-1" value="50" label="Minimum alignment length on each side of the junction." help="May need to be set to smaller values for read lengths smaller than 75bp." argument="--min-chim-overhang" /> |
3
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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39 </inputs> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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40 |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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41 <outputs> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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42 <data name="dr_disco_classify_output" format="tabular" label="${tool.name} on ${dr_disco_detect_output.name}" /> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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43 </outputs> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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44 |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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45 <tests> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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46 <test> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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47 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" /> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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48 <param name="only_valid" value="" /> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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49 |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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50 <output name="dr_disco_classify_output" file="classify_test_16.test-01.out.dbed" ftype="tabular" /> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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51 </test> |
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f2c70d589596
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 3b03a60c8a46cc23f6fbbb9e32111b39c6044fad
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52 |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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53 <test> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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54 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" /> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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55 <param name="only_valid" value="--only-valid" /> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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56 |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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57 <output name="dr_disco_classify_output" file="classify_test_16.test-02.out.dbed" /> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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58 </test> |
5348cfd3ba5c
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59 |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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60 <test> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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61 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" /> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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62 <param name="only_valid" /> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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63 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" /> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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64 |
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65 <output name="dr_disco_classify_output" file="classify_test_16.test-03.out.dbed" ftype="tabular" /> |
5348cfd3ba5c
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66 </test> |
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68 <test> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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69 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" /> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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70 <param name="only_valid" /> |
5348cfd3ba5c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
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71 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" /> |
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72 |
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73 <output name="dr_disco_classify_output" file="classify_test_16.test-04.out.dbed" /> |
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74 </test> |
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75 |
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76 <test> |
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77 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" /> |
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78 <param name="only_valid" /> |
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79 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" /> |
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80 |
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81 <output name="dr_disco_classify_output" file="classify_test_16.test-05.out.dbed" ftype="tabular" /> |
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82 </test> |
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83 <test> |
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84 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" /> |
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85 <param name="only_valid" /> |
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86 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" /> |
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87 |
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88 <output name="dr_disco_classify_output" file="classify_test_16.test-06.out.dbed" /> |
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89 </test> |
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90 <test> |
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91 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" /> |
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92 <param name="only_valid" /> |
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93 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" /> |
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94 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" /> |
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95 |
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96 <output name="dr_disco_classify_output" file="classify_test_16.test-07.out.dbed" ftype="tabular" /> |
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97 </test> |
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98 <test> |
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99 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" /> |
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100 <param name="only_valid" /> |
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101 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" /> |
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102 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" /> |
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103 |
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104 <output name="dr_disco_classify_output" file="classify_test_16.test-08.out.dbed" /> |
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105 </test> |
10
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106 |
3
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107 </tests> |
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108 |
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109 <help><![CDATA[ |
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110 |
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111 **What it does** |
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112 |
11
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113 * Step 3 in dr-disco pipeline |
3
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114 |
11
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115 This tools filters the detected junctions which are likely to be true or false based on a variety of parameters provided in the input table. This filtering is in particular based on variables derived from the shape of the alignment and the ratio of split and spanning reads. |
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116 |
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117 **Attribution** |
3
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118 |
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119 This work is part of Youri Hoogstrate's PhD thesis. |
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120 |
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121 ]]></help> |
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122 |
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123 <expand macro="citations"/> |
11
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124 </tool> |