Mercurial > repos > iuc > control_freec
annotate control_freec.xml @ 2:f923c54a17ee draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
author | iuc |
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date | Sat, 13 Nov 2021 18:28:40 +0000 |
parents | 2c6349fb175c |
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rev | line source |
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2
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
parents:
1
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1 <tool id="control_freec" name="Control-FREEC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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2 <description>detects copy-number changes and allelic imbalances</description> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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3 <macros> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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4 <import>macros.xml</import> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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5 </macros> |
2
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
parents:
1
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6 <expand macro="xrefs"/> |
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
parents:
1
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7 <expand macro="requirements"/> |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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8 <command detect_errors="exit_code"><![CDATA[ |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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9 #if str($reference_source.ref_selector) == 'history': |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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10 ln -s '$reference_source.ref' ./genome.fa && |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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11 samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for control-freec' >&2 && |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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12 #else |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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13 ln -s '$reference_source.ref.fields.path' ./genome.fa && |
1
2c6349fb175c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit a8b671c0a0d277296751dd2ae403603bea1c58dd"
iuc
parents:
0
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14 cp '${reference_source.ref.fields.path}.fai' ./genome.fa.fai && |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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15 #end if |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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16 |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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17 #if int($WGS_WES.advanced_settings.window_section.window) == 0 |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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18 ln -s '$WGS_WES.input_capture_file' ./capture.bed && |
1
2c6349fb175c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit a8b671c0a0d277296751dd2ae403603bea1c58dd"
iuc
parents:
0
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19 |
2c6349fb175c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit a8b671c0a0d277296751dd2ae403603bea1c58dd"
iuc
parents:
0
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20 cat ./capture.bed | cut -f 1 | sort | uniq > ./capture.bed_tmp && |
2c6349fb175c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit a8b671c0a0d277296751dd2ae403603bea1c58dd"
iuc
parents:
0
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21 cp ./genome.fa.fai ./genome.fa.fai_tmp && |
2c6349fb175c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit a8b671c0a0d277296751dd2ae403603bea1c58dd"
iuc
parents:
0
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22 awk 'NR==FNR{A[$1];next}($1 in A)' ./capture.bed_tmp ./genome.fa.fai_tmp > ./genome.fa.fai && |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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23 #end if |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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24 |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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25 mkdir ./chromosomes && |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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26 mkdir ./output && |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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27 |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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28 awk -F " " '/^>/ {close(F); F="chromosomes/"substr($1,2)".fa"} {print >> F}' ./genome.fa && |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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29 |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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30 ln -s '$WGS_WES.input_sample_file' ./sample.bam && |
2
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
parents:
1
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31 #if $WGS_WES.input_control_file |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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32 ln -s '$WGS_WES.input_control_file' ./control.bam && |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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33 #end if |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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34 |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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35 freec |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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36 -conf '$script_file' |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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37 -sample ./sample.bam |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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38 #if $WGS_WES.input_control_file |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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39 -control ./control.bam |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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40 #end if |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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41 |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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42 #if $output_section.makeGraph |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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43 && R -f `which makeGraph.R` '$WGS_WES.advanced_settings.ploidy' 'output/sample.bam_ratio.txt' |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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44 #end if |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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45 |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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46 #if $output_section.circos_data |
1
2c6349fb175c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit a8b671c0a0d277296751dd2ae403603bea1c58dd"
iuc
parents:
0
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47 && python '$__tool_directory__/ratio2circos.py' '$WGS_WES.advanced_settings.ploidy' |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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48 #end if |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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49 ]]></command> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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50 <configfiles> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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51 <configfile name="script_file"><![CDATA[ |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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52 #import os |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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53 #set galaxy_slots = os.getenv("GALAXY_SLOTS", 4) |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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54 [general] |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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55 chrFiles = chromosomes |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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56 outputDir = output |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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57 chrLenFile = genome.fa.fai |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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58 maxThreads = $galaxy_slots |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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59 |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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60 #if $WGS_WES.advanced_settings.degree == "34" |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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61 #set $degree_val = "3&4" |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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62 degree = $degree_val |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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63 #else |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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64 degree = $WGS_WES.advanced_settings.degree |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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65 #end if |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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66 forceGCcontentNormalization = $WGS_WES.advanced_settings.forceGCcontentNormalization |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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67 minCNAlength = $WGS_WES.advanced_settings.minCNAlength |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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68 minimalSubclonePresence = $WGS_WES.advanced_settings.minimalSubclonePresence |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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69 readCountThreshold = $WGS_WES.advanced_settings.readCountThreshold |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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70 window = $WGS_WES.advanced_settings.window_section.window |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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71 step = $WGS_WES.advanced_settings.window_section.step |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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72 coefficientOfVariation = $WGS_WES.advanced_settings.coefficientOfVariation |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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73 #if $output_section.circos_data |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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74 BedGraphOutput = TRUE |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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75 #else |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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76 BedGraphOutput = $output_section.BedGraphOutput |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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77 #end if |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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78 breakPointThreshold = $WGS_WES.advanced_settings.breakPointThreshold |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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79 breakPointType = $WGS_WES.advanced_settings.breakPointType |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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80 contaminationAdjustment = $WGS_WES.advanced_settings.contaminationAdjustment |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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81 contamination = $WGS_WES.advanced_settings.contamination |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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82 intercept = $WGS_WES.advanced_settings.intercept |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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83 minMappabilityPerWindow = $WGS_WES.advanced_settings.minMappabilityPerWindow |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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84 minExpectedGC = $WGS_WES.advanced_settings.minExpectedGC |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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85 maxExpectedGC = $WGS_WES.advanced_settings.maxExpectedGC |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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86 noisyData = $WGS_WES.advanced_settings.noisyData |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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87 ploidy = $WGS_WES.advanced_settings.ploidy |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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88 printNA = $WGS_WES.advanced_settings.printNA |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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89 sex = $WGS_WES.advanced_settings.sex |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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90 telocentromeric = $WGS_WES.advanced_settings.telocentromeric |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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91 |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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92 [sample] |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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93 mateFile = sample.bam |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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94 inputFormat = BAM |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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95 mateOrientation = $WGS_WES.mateOrientation_selector |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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96 |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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97 [control] |
2
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
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1
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98 #if $WGS_WES.input_control_file |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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99 mateFile = control.bam |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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100 inputFormat = BAM |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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101 mateOrientation = $WGS_WES.mateOrientation_selector |
2
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
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1
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102 #end if |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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103 |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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104 #if int($WGS_WES.advanced_settings.window_section.window) == 0 |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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105 [target] |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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106 captureRegions = capture.bed |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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107 #end if |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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108 ]]></configfile> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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109 </configfiles> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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110 <inputs> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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111 <conditional name="WGS_WES"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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112 <param name="WGS_WES_selector" type="select" label="Select the sequencing method of the input file(s)" help=""> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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113 <option value="WGS" selected="True">whole-genome sequencing (WGS)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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114 <option value="WES">whole-exome sequencing (WES)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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115 <option value="other">other method</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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116 </param> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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117 <when value="WGS"> |
2
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
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118 <expand macro="wgs_input_files" /> |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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119 <section name="advanced_settings" title="Advanced WGS settings" expanded="false"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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120 <expand macro="WGS" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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121 <expand macro="shared" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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122 </section> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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123 </when> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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124 <when value="WES"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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125 <expand macro="wes_input_files" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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126 <section name="advanced_settings" title="Advanced WES settings" expanded="false"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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127 <expand macro="WES" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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128 <expand macro="shared" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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129 </section> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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130 </when> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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131 <when value="other"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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132 <expand macro="wes_input_files" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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133 <section name="advanced_settings" title="Advanced settings" expanded="true"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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134 <expand macro="other" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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135 <expand macro="shared" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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136 </section> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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137 </when> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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138 </conditional> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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139 <expand macro="reference_interface" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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140 <expand macro="output_section" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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141 </inputs> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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142 <outputs> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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143 <data name="out_sample_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (sample)" from_work_dir="output/sample.bam_sample.cpn" /> |
2
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
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144 <data name="out_control_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (control)" from_work_dir="output/control.bam_control.cpn"> |
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
parents:
1
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145 <filter>WGS_WES['input_control_file']</filter> |
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
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1
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|
146 </data> |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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147 <data name="out_sample_coord" format="tabular" label="${tool.name} on ${on_string}: Coordinates of predicted CN alterations" from_work_dir="output/sample.bam_CNVs" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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148 <data name="out_sample_info" format="txt" label="${tool.name} on ${on_string}: Information about FREEC run" from_work_dir="output/sample.bam_info.txt" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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149 <data name="out_sample_ratio" format="tabular" label="${tool.name} on ${on_string}: Ratios and predicted CN alterations for each window" from_work_dir="output/sample.bam_ratio.txt" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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150 <data name="out_sample_subclones" format="txt" label="${tool.name} on ${on_string}: Subclones" from_work_dir="output/sample.bam_subclones.txt" > |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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151 <filter>int(WGS_WES['advanced_settings']['minimalSubclonePresence']) != 100</filter> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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152 </data> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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153 <data name="out_sample_bedgraph" format="bed" label="${tool.name} on ${on_string}: Ratios in BedGraph format" from_work_dir="output/sample.bam_ratio.BedGraph"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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154 <filter>output_section['BedGraphOutput']</filter> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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155 </data> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
156 <data name="out_mg_png" format="png" label="${tool.name} on ${on_string}: Normalized CN profile" from_work_dir="output/sample.bam_ratio.txt.png"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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157 <filter>output_section['makeGraph']</filter> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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158 </data> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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159 <data name="out_mg_log2_png" format="png" label="${tool.name} on ${on_string}: Normalized CN profile (log2)" from_work_dir="output/sample.bam_ratio.txt.log2.png"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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160 <filter>output_section['makeGraph']</filter> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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|
161 </data> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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162 <data name="out_gc_profile" format="tabular" label="${tool.name} on ${on_string}: GC-content profile" from_work_dir="output/GC_profile.targetedRegions.cnp"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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163 <filter>int(WGS_WES['advanced_settings']['window_section']['window']) == 0</filter> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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164 </data> |
1
2c6349fb175c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit a8b671c0a0d277296751dd2ae403603bea1c58dd"
iuc
parents:
0
diff
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165 <data name="out_ratio_log2_circos" format="tabular" label="${tool.name} on ${on_string}: Circos Log2 Ratio (2D Data Track)" from_work_dir="output/sample.bam_ratio_log2_circos.txt"> |
2c6349fb175c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit a8b671c0a0d277296751dd2ae403603bea1c58dd"
iuc
parents:
0
diff
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166 <filter>output_section['circos_data']</filter> |
2c6349fb175c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit a8b671c0a0d277296751dd2ae403603bea1c58dd"
iuc
parents:
0
diff
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167 </data> |
2c6349fb175c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit a8b671c0a0d277296751dd2ae403603bea1c58dd"
iuc
parents:
0
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168 <data name="out_chr_sorted_circos" format="tabular" label="${tool.name} on ${on_string}: Circos Karyotype" from_work_dir="output/karyotype_circos.txt"> |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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169 <filter>output_section['circos_data']</filter> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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170 </data> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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171 </outputs> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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172 <tests> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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173 <test expect_num_outputs="5"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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174 <conditional name="reference_source"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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175 <param name="ref_selector" value="history"/> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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176 <param name="ref" ftype="fasta" value="genome.fasta" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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177 </conditional> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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178 <param name="WGS_WES_selector" value="other" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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179 <param name="input_sample_file" ftype="bam" value="tumor.bam" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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180 <param name="input_control_file" ftype="bam" value="normal.bam" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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181 <param name="mateOrientation_selector" value="0" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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182 <param name="window" value="5000" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
183 <param name="step" value="1000" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
184 <output name="out_sample_raw" file="output/sample.bam_sample.cpn" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
185 <output name="out_control_raw" file="output/control.bam_control.cpn" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
186 <output name="out_sample_coord" file="output/sample.bam_CNVs" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
187 <output name="out_sample_info" file="output/sample.bam_info.txt" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
188 <output name="out_sample_ratio" file="output/sample.bam_ratio.txt" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
189 </test> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
190 <test expect_num_outputs="5"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
191 <conditional name="reference_source"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
192 <param name="ref_selector" value="cached"/> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
193 <param name="ref" value="test_buildid"/> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
194 </conditional> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
195 <param name="WGS_WES_selector" value="other" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
196 <param name="input_sample_file" ftype="bam" value="tumor.bam" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
197 <param name="input_control_file" ftype="bam" value="normal.bam" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
198 <param name="mateOrientation_selector" value="0" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
199 <param name="window" value="5000" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
200 <param name="step" value="1000" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
201 <output name="out_sample_raw" file="output/sample.bam_sample.cpn" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
202 <output name="out_control_raw" file="output/control.bam_control.cpn" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
203 <output name="out_sample_coord" file="output/sample.bam_CNVs" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
204 <output name="out_sample_info" file="output/sample.bam_info.txt" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
205 <output name="out_sample_ratio" file="output/sample.bam_ratio.txt" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
206 </test> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
207 <test expect_num_outputs="5"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
208 <conditional name="reference_source"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
209 <param name="ref_selector" value="history"/> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
210 <param name="ref" ftype="fasta" value="genome.fasta" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
211 </conditional> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
212 <param name="WGS_WES_selector" value="WGS" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
213 <param name="input_sample_file" ftype="bam" value="tumor.bam" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
214 <param name="input_control_file" ftype="bam" value="normal.bam" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
215 <param name="mateOrientation_selector" value="0" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
216 <param name="minimalSubclonePresence" value="100" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
217 <param name="window" value="5000" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
218 <param name="step" value="1000" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
219 <output name="out_sample_raw" file="output/sample.bam_sample.cpn" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
220 <output name="out_control_raw" file="output/control.bam_control.cpn" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
221 <output name="out_sample_coord" file="output/sample.bam_CNVs" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
222 <output name="out_sample_info" file="output/sample.bam_info.txt" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
223 <output name="out_sample_ratio" file="output/sample.bam_ratio.txt" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
224 </test> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
225 <test expect_num_outputs="6"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
226 <conditional name="reference_source"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
227 <param name="ref_selector" value="history"/> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
228 <param name="ref" ftype="fasta" value="genome.fasta" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
229 </conditional> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
230 <param name="WGS_WES_selector" value="WES" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
231 <param name="input_sample_file" ftype="bam" value="tumor.bam" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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|
232 <param name="input_control_file" ftype="bam" value="normal.bam" /> |
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233 <param name="input_capture_file" ftype="bed" value="capture.bed" /> |
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234 <param name="mateOrientation_selector" value="0" /> |
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235 <param name="minimalSubclonePresence" value="100" /> |
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236 <param name="forceGCcontentNormalization" value="2" /> |
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237 <param name="window" value="0" /> |
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238 <param name="step" value="0" /> |
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239 <output name="out_sample_raw"> |
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240 <assert_contents> |
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241 <has_text_matching expression="M\t\d+\t\d+\t\d+\tM:\d+-\d+"/> |
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242 </assert_contents> |
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243 </output> |
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244 <output name="out_control_raw"> |
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245 <assert_contents> |
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246 <has_text_matching expression="M\t\d+\t\d+\t\d+\tM:\d+-\d+"/> |
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247 </assert_contents> |
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248 </output> |
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249 <output name="out_sample_coord" file="output/sample.bam_CNVs" /> |
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250 <output name="out_sample_info"> |
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251 <assert_contents> |
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252 <has_text text="Program_Version"/> |
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253 </assert_contents> |
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254 </output> |
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255 <output name="out_sample_ratio"> |
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256 <assert_contents> |
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257 <has_text text="Chromosome"/> |
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258 </assert_contents> |
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259 </output> |
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260 <output name="out_gc_profile" file="output/GC_profile.targetedRegions.cnp" /> |
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261 </test> |
2
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262 <!-- Test without control file--> |
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263 <test expect_num_outputs="4"> |
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264 <conditional name="reference_source"> |
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265 <param name="ref_selector" value="history"/> |
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266 <param name="ref" ftype="fasta" value="genome.fasta" /> |
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267 </conditional> |
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268 <param name="WGS_WES_selector" value="WGS" /> |
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269 <param name="input_sample_file" ftype="bam" value="tumor.bam" /> |
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270 <param name="mateOrientation_selector" value="0" /> |
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271 <param name="minimalSubclonePresence" value="100" /> |
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272 <param name="window" value="50" /> |
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273 <param name="step" value="10" /> |
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274 <output name="out_sample_raw" file="output/sample.bam_sample_woc.cpn" /> |
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275 <output name="out_sample_coord" file="output/sample_woc.bam_CNVs" /> |
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276 <output name="out_sample_info" file="output/sample.bam_info_woc.txt" /> |
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277 <output name="out_sample_ratio" file="output/sample.bam_ratio_woc.txt" /> |
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278 </test> |
0
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279 </tests> |
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280 <help><![CDATA[ |
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281 Control-FREEC |
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282 ============= |
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283 |
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284 Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including loss of heterozygosity/LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). Nowdays, Control-FREEC is supported by the team of Valentina Boeva at Institut Cochin, Inserm (Paris). |
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285 |
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286 Control-FREEC automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. The control (matched normal) sample is optional for whole genome sequencing data but mandatory for whole exome or targeted sequencing data. For whole genome sequencing data analysis, the program can also use mappability data (files created by GEM). |
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287 |
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288 **Input for CNA detection:** Aligned single-end, paired-end or mate-pair data in BAM format. |
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289 |
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290 **Output:** Regions of gain, loss and LOH and normalized copy number. |
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291 |
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292 For more information (f.e. to run Control-FREEC on non-human data) see the Control-FREEC documentation_. |
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293 |
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294 .. _documentation: http://boevalab.inf.ethz.ch/FREEC/index.html#documentation |
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295 |
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296 ]]></help> |
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297 <citations> |
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298 <citation type="doi">10.1093/bioinformatics/btr670</citation> |
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299 <citation type="doi">10.1093/bioinformatics/btq635</citation> |
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300 </citations> |
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301 </tool> |