Mercurial > repos > iuc > cnvkit_batch
annotate batch.xml @ 0:e3bbe8171af9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
author | iuc |
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date | Sun, 14 May 2023 20:10:48 +0000 |
parents | |
children | 4653aeb60243 |
rev | line source |
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0
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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changeset
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1 <tool id="cnvkit_batch" name="CNVkit Batch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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2 <description>Run the CNVkit pipeline on one or more BAM files</description> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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3 <macros> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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changeset
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5 </macros> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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changeset
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6 <expand macro="xrefs"/> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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changeset
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7 <expand macro="requirements"/> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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8 <command detect_errors="exit_code"><![CDATA[ |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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changeset
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9 ln -s '$CNV_reference.input_sample_file' ./tumor.bam && |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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changeset
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10 ln -s '$CNV_reference.input_sample_file.metadata.bam_index' ./tumor.bam.bai && |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
changeset
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11 #if str($CNV_reference.CNV_reference_availabel) == "yes": |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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12 ln -s '$CNV_reference.reference' ./reference.cnn && |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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changeset
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13 #end if |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
changeset
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14 #if str($CNV_reference.CNV_reference_availabel) == "no": |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
changeset
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15 ln -s '$CNV_reference.normal' ./normal.bam && |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
changeset
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16 ln -s '$CNV_reference.normal.metadata.bam_index' ./normal.bam.bai && |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
changeset
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17 #if $CNV_reference.advanced_settings.antitargets |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
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18 ln -s '$CNV_reference.advanced_settings.antitargets' ./antitargets.bed && |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
changeset
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19 #end if |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
changeset
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20 #if $CNV_reference.advanced_settings.annotate |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
changeset
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21 ln -s '$CNV_reference.advanced_settings.annotate' ./annotate.bed && |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
changeset
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22 #end if |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
changeset
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23 #if $CNV_reference.advanced_settings.access |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
changeset
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24 ln -s '$CNV_reference.advanced_settings.access' ./access.bed && |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
changeset
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25 #end if |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
changeset
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26 ln -s '$CNV_reference.targets' ./capture.bed && |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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changeset
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27 #if str($CNV_reference.reference_source.ref_selector) == 'history': |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
changeset
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28 ln -s '$CNV_reference.reference_source.fasta' ./genome.fa && |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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changeset
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29 samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for CNVkit' >&2 && |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
changeset
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30 #else |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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changeset
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31 ln -s '$CNV_reference.reference_source.fasta.fields.path' ./genome.fa && |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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32 ln -s '${CNV_reference.reference_source.fasta.fields.path}.fai' ./genome.fa.fai && |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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33 #end if |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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34 #end if |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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35 #import os |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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36 cnvkit.py batch |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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37 ./tumor.bam |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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38 #if str($CNV_reference.CNV_reference_availabel) == "no": |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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39 --normal ./normal.bam |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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40 --targets ./capture.bed |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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41 --fasta ./genome.fa |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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42 #if $CNV_reference.advanced_settings.antitargets |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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43 --antitargets ./antitargets.bed |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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44 #end if |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
diff
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45 #if $CNV_reference.advanced_settings.annotate |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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46 --annotate ./annotate.bed |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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47 #end if |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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48 #if $CNV_reference.advanced_settings.access |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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49 --access ./access.bed |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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50 #end if |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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51 #end if |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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52 #if str($CNV_reference.CNV_reference_availabel) == "yes": |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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53 --reference ./reference.cnn |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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54 #end if |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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55 $output_section.scatter |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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56 $output_section.diagram |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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57 --processes \${GALAXY_SLOTS:-4} |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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58 #if $CNV_reference.advanced_settings.method == "hybrid" |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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59 #set $method_val = "hybrid" |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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60 --method '$method_val' |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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61 #else |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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62 --method '$CNV_reference.advanced_settings.method' |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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63 #end if |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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64 |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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65 #if $CNV_reference.advanced_settings.segment_method == "cbs" |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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66 #set $segment_method_val = "cbs" |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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67 --segment-method '$segment_method_val' |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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68 #else |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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69 --segment-method '$CNV_reference.advanced_settings.segment_method' |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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70 #end if |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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71 $CNV_reference.advanced_settings.male_reference |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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72 $CNV_reference.advanced_settings.countreads |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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73 $CNV_reference.advanced_settings.drop_low_coverage |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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74 |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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75 #if str($CNV_reference.CNV_reference_availabel) == "no": |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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76 $CNV_reference.advanced_settings.short_names |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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77 #if str($CNV_reference.advanced_settings.target_avg_size) |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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78 --target-avg-size $CNV_reference.advanced_settings.target_avg_size |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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79 #end if |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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80 #if str($CNV_reference.advanced_settings.antitarget_avg_size) |
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81 --antitarget-avg-size $CNV_reference.advanced_settings.antitarget_avg_size |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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82 #end if |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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83 #if str($CNV_reference.advanced_settings.antitarget_min_size) |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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84 --antitarget-min-size $CNV_reference.advanced_settings.antitarget_min_size |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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85 #end if |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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86 $CNV_reference.advanced_settings.cluster |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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87 #end if |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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88 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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89 <inputs> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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90 <conditional name="CNV_reference"> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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91 <param name="CNV_reference_availabel" type="select" label="Build or reuse a copy number reference file (.cnn)?" help=""> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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92 <option value="no" selected="True">Build a new copy number reference file</option> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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93 <option value="yes">Reuse a copy number reference file</option> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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94 </param> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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95 <when value="no"> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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96 <expand macro="create_CNV_reference_file" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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97 <expand macro="reference_interface" /> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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98 <section name="advanced_settings" title="Advanced settings" expanded="false"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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99 <expand macro="advanced_no_reference" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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100 <expand macro="shared" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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101 </section> |
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102 </when> |
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103 <when value="yes"> |
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104 <expand macro="reuse_an_existing_cnv_reference_file" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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105 <section name="advanced_settings" title="Advanced settings" expanded="false"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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106 <expand macro="shared" /> |
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107 </section> |
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108 </when> |
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109 </conditional> |
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110 <expand macro="output_section" /> |
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111 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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112 <outputs> |
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113 <data name="out_sample_bintest" format="tabular" label="${tool.name} on ${on_string}: Sample Bintest" from_work_dir="tumor.bintest.cns" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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114 <data name="out_sample_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Sample Antitarget Coverage" from_work_dir="tumor.antitargetcoverage.cnn" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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115 <data name="out_sample_call" format="tabular" label="${tool.name} on ${on_string}: rounded absolute scale copy numbers integer (not log2 ratios) " from_work_dir="tumor.call.cns" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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116 <data name="out_sample_targetcoverage_cnn" format="tabular" label="${tool.name} on ${on_string}: Sample Target Coverage" from_work_dir="tumor.targetcoverage.cnn" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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117 <data name="out_sample_cns" format="tabular" label="${tool.name} on ${on_string}: CN segmentation calls" from_work_dir="tumor.cns" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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118 <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="tumor.cnr" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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119 <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: Capture Antitarget" from_work_dir="capture.antitarget.bed"> |
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120 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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121 </data> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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122 <data name="out_control_targetcoverage" format="tabular" label="${tool.name} on ${on_string}: Output Normal Sample Target Coverage" from_work_dir="normal.targetcoverage.cnn"> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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123 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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124 </data> |
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125 <data name="out_control_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Output Normal Sample Antitarget Coverage" from_work_dir="normal.antitargetcoverage.cnn"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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126 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter> |
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127 </data> |
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128 <data name="out_reference_cnn" format="tabular" label="${tool.name} on ${on_string}: Output Copy Number Reference Profile" from_work_dir="reference.cnn"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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129 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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130 </data> |
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131 <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: Output Capture Target" from_work_dir="capture.target.bed"> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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132 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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133 </data> |
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134 <data name="out_reference_target_bed" format="tabular" label="${tool.name} on ${on_string}: Output Reference Target" from_work_dir="reference.target-tmp.bed"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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135 <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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136 </data> |
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137 <data name="out_reference_antitarget_bed" format="bed" label="${tool.name} on ${on_string}: Output Reference Antitarget" from_work_dir="reference.antitarget-tmp.bed"> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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138 <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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139 </data> |
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140 <data name="out_sample_diagram_pdf" format="pdf" label="${tool.name} on ${on_string}: Output Sample Diagram" from_work_dir="tumor-diagram.pdf"> |
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141 <filter>output_section['diagram']</filter> |
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142 </data> |
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143 <data name="out_sample_scatter_png" format="png" label="${tool.name} on ${on_string}: Output Sample Scatter " from_work_dir="tumor-scatter.png"> |
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144 <filter>output_section['scatter']</filter> |
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145 </data> |
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146 </outputs> |
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147 <tests> |
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148 <test expect_num_outputs="13"> |
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149 <conditional name="reference_source"> |
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150 <param name="ref_selector" value="history"/> |
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151 <param name="fasta" ftype="fasta" value="genome.fasta" /> |
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152 </conditional> |
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153 <param name="CNV_reference_availabel" value="no" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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154 <param name="input_sample_file" ftype="bam" value="tumor.bam" /> |
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155 <param name="normal" ftype="bam" value="normal.bam" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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156 <param name="targets" ftype="bed" value="capture.bed" /> |
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157 <param name="scatter" value="1"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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158 <param name="diagram" value="1"/> |
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159 <output name="out_sample_bintest" file="tumor.bintest.cns" /> |
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160 <output name="out_sample_antitargetcoverage"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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161 <assert_contents><has_text text="chromosome"/></assert_contents> |
e3bbe8171af9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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162 </output> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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163 <output name="out_sample_call"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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164 <assert_contents><has_text text="chromosome"/></assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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165 </output> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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166 <output name="out_sample_cnr"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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167 <assert_contents><has_text text="chromosome"/></assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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168 </output> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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169 <output name="out_sample_targetcoverage_cnn"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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170 <assert_contents><has_text text="chromosome"/></assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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171 </output> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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172 <output name="out_sample_cns"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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173 <assert_contents><has_text text="chromosome"/></assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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174 </output> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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175 <output name="out_capture_antitarget" file="capture.antitarget.bed" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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176 <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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177 <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" /> |
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178 <output name="out_reference_cnn" file="reference.cnn" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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179 <output name="out_capture_target"> |
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180 <assert_contents><has_text_matching expression="chrM"/></assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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181 </output> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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182 <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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183 <assert_contents><has_size value="13000" delta="3000" /></assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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184 </output> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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185 <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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186 <assert_contents><has_size value="6000" delta="2000" /></assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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187 </output> |
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188 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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189 <test expect_num_outputs="13"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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190 <conditional name="reference_source"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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191 <param name="ref_selector" value="cached"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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192 <param name="fasta" value="test_buildid"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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193 </conditional> |
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194 <param name="CNV_reference_availabel" value="no" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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195 <param name="input_sample_file" ftype="bam" value="tumor.bam" /> |
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196 <param name="normal" ftype="bam" value="normal.bam" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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197 <param name="targets" ftype="bed" value="capture.bed" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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198 <param name="scatter" value="1"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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199 <param name="diagram" value="1"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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200 <output name="out_sample_bintest" file="tumor.bintest.cns" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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201 <output name="out_sample_antitargetcoverage"> |
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202 <assert_contents><has_text text="chromosome"/></assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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203 </output> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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204 <output name="out_sample_call"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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205 <assert_contents><has_text text="chromosome"/></assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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206 </output> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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207 <output name="out_sample_cnr"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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208 <assert_contents><has_text text="chromosome"/></assert_contents> |
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209 </output> |
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210 <output name="out_sample_targetcoverage_cnn"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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211 <assert_contents><has_text text="chromosome"/></assert_contents> |
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212 </output> |
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213 <output name="out_sample_cns"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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214 <assert_contents><has_text text="chromosome"/></assert_contents> |
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215 </output> |
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216 <output name="out_capture_antitarget" file="capture.antitarget.bed" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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217 <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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218 <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" /> |
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219 <output name="out_reference_cnn" file="reference.cnn" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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220 <output name="out_capture_target"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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221 <assert_contents><has_text_matching expression="chrM"/></assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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222 </output> |
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223 <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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224 <assert_contents><has_size value="13000" delta="3000" /></assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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225 </output> |
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226 <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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227 <assert_contents><has_size value="6000" delta="2000" /></assert_contents> |
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228 </output> |
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229 </test> |
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230 <test expect_num_outputs="10"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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231 <param name="CNV_reference_availabel" value="yes" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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232 <param name="input_sample_file" ftype="bam" value="tumor.bam" /> |
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233 <param name="reference" ftype="tabular" value="reference.cnn" /> |
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234 <param name="scatter" value="1"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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235 <param name="diagram" value="1"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
parents:
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236 <output name="out_sample_bintest" file="tumor.bintest.cns" /> |
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237 <output name="out_sample_antitargetcoverage"> |
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238 <assert_contents><has_text text="chromosome"/></assert_contents> |
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239 </output> |
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240 <output name="out_sample_call"> |
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241 <assert_contents><has_text text="chromosome"/></assert_contents> |
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242 </output> |
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243 <output name="out_sample_cnr"> |
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244 <assert_contents><has_text text="chromosome"/></assert_contents> |
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245 </output> |
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246 <output name="out_sample_targetcoverage_cnn"> |
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247 <assert_contents><has_text text="chromosome"/></assert_contents> |
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248 </output> |
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249 <output name="out_sample_cns"> |
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250 <assert_contents><has_text text="chromosome"/></assert_contents> |
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251 </output> |
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252 <output name="out_reference_target_bed" file="reference.target-tmp.bed" /> |
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253 <output name="out_reference_antitarget_bed" file="reference.antitarget-tmp.bed" /> |
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254 <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size"> |
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255 <assert_contents><has_size value="6000" delta="2000" /></assert_contents> |
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256 </output> |
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257 <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size"> |
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258 <assert_contents><has_size value="13000" delta="3000" /></assert_contents> |
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259 </output> |
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260 </test> |
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261 </tests> |
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262 <help><![CDATA[ |
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263 CNVkit pipeline for copy-number changes and allelic imbalances detection |
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264 cnn, cnr and cns are tabuler files extintions: |
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265 |
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266 The reference .cnn file has the columns: |
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267 chromosome, Start, end, gene, GC content of the sequence region (gc), RepeatMasker-masked proportion |
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268 of the sequence region (rmask), Statistical spread or dispersion (spread), Robust average of coverage |
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269 depths (log2 ) and Robust average of absolute-scale coverage depths without any bias corrections (depth) |
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270 |
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271 Target and antitarget bin-level coverages (.cnn) |
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272 chromosome, Start, end, gene, log2 and depth |
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273 |
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274 Bin-level log2 ratios (.cnr) |
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275 chromosome, Start, end, gene, log2, depth and proportional weight or reliability (weight) |
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276 |
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277 Segmented log2 ratios (.cns) |
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278 chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes) |
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279 |
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280 |
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281 ]]></help> |
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282 <expand macro="citations" /> |
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283 </tool> |