Mercurial > repos > iuc > control_freec
annotate macros.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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0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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1 <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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2 <token name="@VERSION_SUFFIX@">2</token> |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
3 <token name="@TOOL_VERSION@">11.6</token> |
2
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
parents:
1
diff
changeset
|
4 <xml name="requirements"> |
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
parents:
1
diff
changeset
|
5 <requirements> |
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
parents:
1
diff
changeset
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6 <requirement type="package" version="5.0.1">gawk</requirement> |
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
parents:
1
diff
changeset
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7 <requirement type="package" version="@TOOL_VERSION@">control-freec</requirement> |
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
parents:
1
diff
changeset
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8 </requirements> |
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
parents:
1
diff
changeset
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9 </xml> |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
10 <xml name="reference_interface"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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11 <conditional name="reference_source"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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12 <param name="ref_selector" type="select" label="Choose the source for the reference genome"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
13 <option value="cached">Locally cached</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
14 <option value="history">History</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
15 </param> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
16 <when value="cached"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
17 <param argument="--ref" type="select" label="Reference genome"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
18 <options from_data_table="fasta_indexes"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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19 <!-- <filter type="data_meta" column="dbkey" key="dbkey" ref="input_sample_file" /> --> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
20 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
21 </options> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
22 </param> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
23 </when> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
24 <when value="history"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
25 <param argument="--ref" type="data" format="fasta" label="Reference" help="Reference sequence" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
26 </when> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
27 </conditional> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
28 </xml> |
2
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
parents:
1
diff
changeset
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29 <xml name="xrefs"> |
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
parents:
1
diff
changeset
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30 <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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changeset
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31 <xref type="bio.tools">freec</xref> |
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
parents:
1
diff
changeset
|
32 </xrefs> |
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
iuc
parents:
1
diff
changeset
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33 </xml> |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
34 <xml name="WGS"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
35 <param name="degree" type="select" label="Degree of polynomial" help=""> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
36 <option value="34" selected="True">GC-content based normalization, WGS (3&4)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
37 <option value="1">control-read-count-based normalization, WES (1)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
38 </param> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
39 <param name="forceGCcontentNormalization" type="select" label="Read Count (RC) correction for GC-content bias and low mappability" help="Set to 1 or 2 to correct the Read Count (RC) for GC-content bias and low mappability even when you have a control sample. - Default (WGS): 0 - Default (WES): 1"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
40 <option value="0" selected="True">simply model "sample RC ~ Control RC" (0)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
41 <option value="1">normalize the sample and the control RC using GC-content and then calculate the ratio "Sample RC/contol RC" (1)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
42 <option value="2">model "sample RC ~ Control RC" bias, and then normalize for GC-content (2)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
43 </param> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
44 <param name="minCNAlength" type="select" label="Minimal number of consecutive windows to call a CNA" help=""> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
45 <option value="1" selected="True">WGS (1)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
46 <option value="3">WES (3)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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47 </param> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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48 <param name="minimalSubclonePresence" type="integer" label="Detects subclones present in x% of cell population" value="20" help="Default: 100 (meaning "do not look for subclones") Suggested: 20 for WGS and 30 for WES." /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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49 <param name="readCountThreshold" type="integer" label="Threshold on the minimal number of reads per window" value="10" help="Threshold on the minimal number of reads per window in the control sample. Useful for exome-seq or targeted sequencing data. Default: 10 recommended value >=50 for for exome data." /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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50 <section name="window_section" title="Select window size" expanded="true"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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51 <param name="window" type="integer" value="50000" label="Explicit window size" help="Higher priority than coefficientOfVariation. Ex: for whole genome sequencing: "50000"; for whole exome sequencing: "0"" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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52 <param name="step" type="integer" value="10000" label="Step" help="Used only when "window" is specified. Do not use for exome sequencing (instead set "0"). Ex: 10000" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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53 </section> |
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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54 <param name="printNA" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Print NA to avoid "-1"" help="Set "No" to avoid printing "-1" to the _ratio.txt files. Useful for exome-seq or targeted sequencing data." /> |
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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55 <param name="noisyData" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Noisy Data" help="Set "Yes" for target resequencing data (e.g., exome-seq) to avoid false positive predictions due to non-uniform capture" /> |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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56 </xml> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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57 <xml name="WES"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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58 <param name="degree" type="select" label="Degree of polynomial" help=""> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
59 <option value="34">GC-content based normalization, WGS (3&4)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
60 <option value="1" selected="True">control-read-count-based normalization, WES (1)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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61 </param> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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62 <param name="forceGCcontentNormalization" type="select" label="Read Count (RC) correction for GC-content bias and low mappability" help="Set to 1 or 2 to correct the Read Count (RC) for GC-content bias and low mappability even when you have a control sample. - Default (WGS): 0 - Default (WES): 1"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
63 <option value="0">simply model "sample RC ~ Control RC" (0)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
64 <option value="1" selected="True">normalize the sample and the control RC using GC-content and then calculate the ratio "Sample RC/contol RC" (1)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
65 <option value="2">model "sample RC ~ Control RC" bias, and then normalize for GC-content (2)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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66 </param> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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67 <param name="minCNAlength" type="select" label="Minimal number of consecutive windows to call a CNA" help=""> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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68 <option value="1">WGS (1)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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69 <option value="3" selected="True">WES (3)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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70 </param> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
71 <param name="minimalSubclonePresence" type="integer" label="Detects subclones present in x% of cell population" value="30" help="Default: 100 (meaning "do not look for subclones") Suggested: 20 for WGS and 30 for WES." /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
|
72 <param name="readCountThreshold" type="integer" label="Threshold on the minimal number of reads per window" value="50" help="Threshold on the minimal number of reads per window in the control sample. Useful for exome-seq or targeted sequencing data. Default: 10 recommended value >=50 for for exome data." /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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73 <section name="window_section" title="Select window size" expanded="false"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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74 <param name="window" type="integer" value="0" label="Explicit window size" help="Higher priority than coefficientOfVariation. Ex: for whole genome sequencing: "50000"; for whole exome sequencing: "0"" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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75 <param name="step" type="integer" value="0" label="Step" help="Used only when "window" is specified. Do not use for exome sequencing (instead set "0"). Ex: 10000" /> |
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76 </section> |
1
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77 <param name="printNA" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Print NA to avoid "-1"" help="Set "No" to avoid printing "-1" to the _ratio.txt files. Useful for exome-seq or targeted sequencing data." /> |
2c6349fb175c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit a8b671c0a0d277296751dd2ae403603bea1c58dd"
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78 <param name="noisyData" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Noisy Data" help="Set "Yes" for target resequencing data (e.g., exome-seq) to avoid false positive predictions due to non-uniform capture" /> |
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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79 </xml> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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80 <xml name="other"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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81 <param name="degree" type="select" label="Degree of polynomial" help=""> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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82 <option value="34" selected="True">GC-content based normalization, WGS (3&4)</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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83 <option value="1">control-read-count-based normalization, WES (1)</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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84 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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85 <param name="forceGCcontentNormalization" type="select" label="Read Count (RC) correction for GC-content bias and low mappability" help="Set to 1 or 2 to correct the Read Count (RC) for GC-content bias and low mappability even when you have a control sample. - Default (WGS): 0 - Default (WES): 1"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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86 <option value="0" selected="True">simply model "sample RC ~ Control RC" (0)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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87 <option value="1">normalize the sample and the control RC using GC-content and then calculate the ratio "Sample RC/contol RC" (1)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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88 <option value="2">model "sample RC ~ Control RC" bias, and then normalize for GC-content (2)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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89 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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90 <param name="minCNAlength" type="select" label="Minimal number of consecutive windows to call a CNA" help=""> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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91 <option value="1" selected="True">WGS (1)</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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92 <option value="3">WES (3)</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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93 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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94 <param name="minimalSubclonePresence" type="integer" label="Detects subclones present in x% of cell population" value="100" help="Default: 100 (meaning "do not look for subclones") Suggested: 20 for WGS and 30 for WES." /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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95 <param name="readCountThreshold" type="integer" label="Threshold on the minimal number of reads per window" value="10" help="Threshold on the minimal number of reads per window in the control sample. Useful for exome-seq or targeted sequencing data. Default: 10 recommended value >=50 for for exome data." /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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96 <section name="window_section" title="Select window size" expanded="true"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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97 <param name="window" type="integer" value="50000" label="Explicit window size" help="Higher priority than coefficientOfVariation. Ex: for whole genome sequencing: "50000"; for whole exome sequencing: "0"" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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98 <param name="step" type="integer" value="10000" label="Step" help="Used only when "window" is specified. Do not use for exome sequencing (instead set "0"). Ex: 10000" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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99 </section> |
1
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100 <param name="printNA" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Print NA to avoid "-1"" help="Set "No" to avoid printing "-1" to the _ratio.txt files. Useful for exome-seq or targeted sequencing data." /> |
2c6349fb175c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit a8b671c0a0d277296751dd2ae403603bea1c58dd"
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101 <param name="noisyData" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Noisy Data" help="Set "Yes" for target resequencing data (e.g., exome-seq) to avoid false positive predictions due to non-uniform capture" /> |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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102 </xml> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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103 <xml name="shared"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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104 <!-- general parameters --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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105 <param name="breakPointThreshold" type="float" label="Segmentation of normalized profiles (break point)" value="0.8" help="Positive value of threshold for segmentation of normalized profiles. Use something like 0.6 to get more segments (and thus more predicted CNVs)." /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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106 <param name="breakPointType" type="select" label="Desired behavior in the ambiguous regions"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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107 <option value="0" selected="true">the "unknown" region is attached to the "known" region on the right (0)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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108 <option value="1">make a separate fragment of this "unknown" region and then attaches it to the left or to the right region choosing the longer one (1)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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109 <option value="2">make a separate fragment of this "unknown" region and then attaches it to the left or to the right region but the "ploidy" copy number has a priority (2)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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110 <option value="3">make a separate fragment of this "unknown" region and then attaches it to the left or to the right region choosing the longer one but this "known" region should make at least half-size of the "unknown" region (3)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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111 <option value="4">make a separate fragment of this "unknown" region and do not assign any copy number to this region at all (4)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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112 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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113 <param name="coefficientOfVariation" type="float" label="Coefficient of variation to evaluate necessary window size" value="0.05" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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114 <param name="contaminationAdjustment" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Adjust sample contamination?" help="a priori known value of tumor sample contamination by normal cells. Set "Yes" to correct for contamination by normal cells. If "contamination" is not provided, it will automatically evaluate the level of contamination." /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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115 <param name="contamination" type="float" label="Sample contamination by normal cells" value="0" help="Ex: contamination=0.25" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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116 <!-- GCcontentProfile --> |
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117 <!-- gemMappabilityFile --> |
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118 <param name="intercept" type="select" label="Intercept of polynomial" help=""> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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119 <option value="0">with a control dataset (0)</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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120 <option value="1" selected="True">with GC-content (1)</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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121 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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122 <param name="minMappabilityPerWindow" type="float" label="Minimal mappability per window" value="0.85" min="0" max="1" help="Only windows with fraction of mappable positions higher than or equal to this threshold will be considered (if "gemMappabilityFile" is not provided, one uses the percentage of non-N letters per window)" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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123 <param name="minExpectedGC" type="float" label="Minimal expected value of the GC-content" value="0.35" min="0" max="1" help="Minimal expected value of the GC-content for the prior evaluation of "Read Count ~ GC-content" dependency. Change only if you run Control-FREEC on a bacterial genome." /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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124 <param name="maxExpectedGC" type="float" label="Maximal expected value of the GC-content" value="0.55" min="0" max="1" help="Maximal expected value of the GC-content for the prior evaluation of "Read Count ~ GC-content" dependency. Change only if you run Control-FREEC on a bacterial genome." /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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125 <param name="ploidy" type="text" value="2" label="Genome ploidy" help="In case of doubt, you can set different values and Control-FREEC will select the one that explains most observed CNAs. Ex: 2 or 2,3,4" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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126 <param name="sex" type="select" label="Sample sex" help=""XX" will exclude chr Y from the analysis. "XY" will not annotate one copy of chr X and Y as a loss."> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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127 <option value="XY" selected="True">XY</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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128 <option value="XX">XX</option> |
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129 <option value="no value">Do not expecify sex</option> |
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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130 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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131 <param name="telocentromeric" type="integer" value="50000" label="Length of pre-telomeric and pre-centromeric regions" help="Control-FREEC will not output small CNAs and LOH found within these regions (they are likely to be false because of mappability/genome assembly issues). 50000 is OK for human/mouse genomes. Use smaller values for yeasts and flies. Do not set anything for exome-seq data." /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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132 <!-- uniqueMatch if true -> gemMappabilityFile is needed--> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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133 <!-- BAF parameters --> |
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134 <!-- makePileup: path to a BED or VCF file with SNP positions --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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135 <!-- fastaFile --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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136 <!-- minimalCoveragePerPosition --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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137 <!-- minimalQualityPerPosition --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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138 <!-- shiftInQuality --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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139 <!-- SNPfile --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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140 </xml> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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141 <xml name="mateOrientation_selector"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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142 <param name="mateOrientation_selector" type="select" display="radio" label="Format of reads" help="If you specify orientation of your reads then only reads mapping in the corresponding orientation will be used for calculation of copy number profiles."> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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143 <option value="0" selected="True">single-end (0)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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144 <option value="RF">Illumina mate-pair (RF)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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145 <option value="FR">Illumina paired-end (FR)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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146 <option value="FF">SOLiD mate-pair (FF)</option> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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147 </param> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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148 </xml> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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149 <xml name="input_control_sample"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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150 <param name="input_sample_file" type="data" format="bam" multiple="false" label="Sample file" help="Sample file in .BAM format." /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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151 <param name="input_control_file" type="data" format="bam" multiple="false" label="Control file" help="Control file in .BAM format." /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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152 </xml> |
2
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
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153 <xml name="input_control_sample_wgs"> |
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
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154 <param name="input_sample_file" type="data" format="bam" multiple="false" label="Sample file" help="Sample file in .BAM format." /> |
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
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155 <param name="input_control_file" type="data" format="bam" multiple="false" optional="true" label="Control file" help="Control file in .BAM format." /> |
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
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156 </xml> |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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157 <xml name="wes_input_files"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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158 <expand macro="input_control_sample" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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159 <param name="input_capture_file" optional="true" type="data" format="bed" multiple="false" label="BED file with capture regions" help="Capture regions in .BED format." /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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160 <expand macro="mateOrientation_selector" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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161 </xml> |
2
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
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162 <xml name="wgs_input_files"> |
f923c54a17ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
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163 <expand macro="input_control_sample_wgs" /> |
0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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164 <expand macro="mateOrientation_selector" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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165 </xml> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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166 <xml name="output_section"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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167 <section name="output_section" title="Outputs" expanded="false"> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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168 <param name="BedGraphOutput" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="BedGraph Output for UCSC genome browser" help="Set "Yes" if you want an additional output in BedGraph format for the UCSC genome browser." /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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169 <param name="makeGraph" type="boolean" checked="false" label="Visualize normalized copy number profile with predicted CNAs" help="Currently only human genomes are supported!" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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170 <param name="circos_data" type="boolean" checked="false" label="2D data track file for Circos" help="Output: chrName startPos endPos log2Ratio" /> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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171 </section> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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172 </xml> |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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173 </macros> |