| Previous changeset 1:2c6349fb175c (2020-08-18) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b" |
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modified:
control_freec.xml macros.xml |
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added:
test-data/output/sample.bam_info_woc.txt test-data/output/sample.bam_ratio_woc.txt test-data/output/sample.bam_sample_woc.cpn test-data/output/sample_woc.bam_CNVs |
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| diff -r 2c6349fb175c -r f923c54a17ee control_freec.xml --- a/control_freec.xml Tue Aug 18 08:52:45 2020 -0400 +++ b/control_freec.xml Sat Nov 13 18:28:40 2021 +0000 |
| [ |
| @@ -1,12 +1,10 @@ -<tool id="control_freec" name="Control-FREEC" version="@WRAPPER_VERSION@"> +<tool id="control_freec" name="Control-FREEC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>detects copy-number changes and allelic imbalances</description> <macros> <import>macros.xml</import> </macros> - <requirements> - <requirement type="package" version="5.0.1">gawk</requirement> - <requirement type="package" version="@TOOL_VERSION@">control-freec</requirement> - </requirements> + <expand macro="xrefs"/> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ #if str($reference_source.ref_selector) == 'history': ln -s '$reference_source.ref' ./genome.fa && @@ -30,7 +28,7 @@ awk -F " " '/^>/ {close(F); F="chromosomes/"substr($1,2)".fa"} {print >> F}' ./genome.fa && ln -s '$WGS_WES.input_sample_file' ./sample.bam && - #if $input_control_file + #if $WGS_WES.input_control_file ln -s '$WGS_WES.input_control_file' ./control.bam && #end if @@ -97,9 +95,11 @@ mateOrientation = $WGS_WES.mateOrientation_selector [control] +#if $WGS_WES.input_control_file mateFile = control.bam inputFormat = BAM mateOrientation = $WGS_WES.mateOrientation_selector +#end if #if int($WGS_WES.advanced_settings.window_section.window) == 0 [target] @@ -115,7 +115,7 @@ <option value="other">other method</option> </param> <when value="WGS"> - <expand macro="def_input_files" /> + <expand macro="wgs_input_files" /> <section name="advanced_settings" title="Advanced WGS settings" expanded="false"> <expand macro="WGS" /> <expand macro="shared" /> @@ -141,7 +141,9 @@ </inputs> <outputs> <data name="out_sample_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (sample)" from_work_dir="output/sample.bam_sample.cpn" /> - <data name="out_control_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (control)" from_work_dir="output/control.bam_control.cpn" /> + <data name="out_control_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (control)" from_work_dir="output/control.bam_control.cpn"> + <filter>WGS_WES['input_control_file']</filter> + </data> <data name="out_sample_coord" format="tabular" label="${tool.name} on ${on_string}: Coordinates of predicted CN alterations" from_work_dir="output/sample.bam_CNVs" /> <data name="out_sample_info" format="txt" label="${tool.name} on ${on_string}: Information about FREEC run" from_work_dir="output/sample.bam_info.txt" /> <data name="out_sample_ratio" format="tabular" label="${tool.name} on ${on_string}: Ratios and predicted CN alterations for each window" from_work_dir="output/sample.bam_ratio.txt" /> @@ -257,6 +259,23 @@ </output> <output name="out_gc_profile" file="output/GC_profile.targetedRegions.cnp" /> </test> + <!-- Test without control file--> + <test expect_num_outputs="4"> + <conditional name="reference_source"> + <param name="ref_selector" value="history"/> + <param name="ref" ftype="fasta" value="genome.fasta" /> + </conditional> + <param name="WGS_WES_selector" value="WGS" /> + <param name="input_sample_file" ftype="bam" value="tumor.bam" /> + <param name="mateOrientation_selector" value="0" /> + <param name="minimalSubclonePresence" value="100" /> + <param name="window" value="50" /> + <param name="step" value="10" /> + <output name="out_sample_raw" file="output/sample.bam_sample_woc.cpn" /> + <output name="out_sample_coord" file="output/sample_woc.bam_CNVs" /> + <output name="out_sample_info" file="output/sample.bam_info_woc.txt" /> + <output name="out_sample_ratio" file="output/sample.bam_ratio_woc.txt" /> + </test> </tests> <help><![CDATA[ Control-FREEC |
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| diff -r 2c6349fb175c -r f923c54a17ee macros.xml --- a/macros.xml Tue Aug 18 08:52:45 2020 -0400 +++ b/macros.xml Sat Nov 13 18:28:40 2021 +0000 |
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| @@ -1,6 +1,12 @@ <macros> - <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@TOOL_VERSION@">11.6</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="5.0.1">gawk</requirement> + <requirement type="package" version="@TOOL_VERSION@">control-freec</requirement> + </requirements> + </xml> <xml name="reference_interface"> <conditional name="reference_source"> <param name="ref_selector" type="select" label="Choose the source for the reference genome"> @@ -20,6 +26,11 @@ </when> </conditional> </xml> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">freec</xref> + </xrefs> + </xml> <xml name="WGS"> <param name="degree" type="select" label="Degree of polynomial" help=""> <option value="34" selected="True">GC-content based normalization, WGS (3&4)</option> @@ -115,7 +126,7 @@ <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."> <option value="XY" selected="True">XY</option> <option value="XX">XX</option> - <option value="no value"></option> + <option value="no value">Do not expecify sex</option> </param> <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." /> <!-- uniqueMatch if true -> gemMappabilityFile is needed--> @@ -139,13 +150,17 @@ <param name="input_sample_file" type="data" format="bam" multiple="false" label="Sample file" help="Sample file in .BAM format." /> <param name="input_control_file" type="data" format="bam" multiple="false" label="Control file" help="Control file in .BAM format." /> </xml> + <xml name="input_control_sample_wgs"> + <param name="input_sample_file" type="data" format="bam" multiple="false" label="Sample file" help="Sample file in .BAM format." /> + <param name="input_control_file" type="data" format="bam" multiple="false" optional="true" label="Control file" help="Control file in .BAM format." /> + </xml> <xml name="wes_input_files"> <expand macro="input_control_sample" /> <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." /> <expand macro="mateOrientation_selector" /> </xml> - <xml name="def_input_files"> - <expand macro="input_control_sample" /> + <xml name="wgs_input_files"> + <expand macro="input_control_sample_wgs" /> <expand macro="mateOrientation_selector" /> </xml> <xml name="output_section"> |
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| diff -r 2c6349fb175c -r f923c54a17ee test-data/output/sample.bam_info_woc.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/sample.bam_info_woc.txt Sat Nov 13 18:28:40 2021 +0000 |
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| @@ -0,0 +1,13 @@ +Program_Version v11.6 +Sample_Name sample.bam +Control_Used False +CGcontent_Used True +Mappability_Used False +Looking_For_Subclones False +Breakpoint_Threshold 0.8 +Window 50 +Number_Of_Reads|Pairs_In_Sample 657 +Number_Of_Reads|Pairs_In_Control 0 +Output_Ploidy 2 +Sample_Purity 1 +Good_Polynomial_Fit True |
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| diff -r 2c6349fb175c -r f923c54a17ee test-data/output/sample.bam_ratio_woc.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/sample.bam_ratio_woc.txt Sat Nov 13 18:28:40 2021 +0000 |
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| b'@@ -0,0 +1,1659 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|
| b |
| diff -r 2c6349fb175c -r f923c54a17ee test-data/output/sample.bam_sample_woc.cpn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/sample.bam_sample_woc.cpn Sat Nov 13 18:28:40 2021 +0000 |
| b |
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t16560\t16609\t0\n+M\t16570\t16619\t0\n' |
| b |
| diff -r 2c6349fb175c -r f923c54a17ee test-data/output/sample_woc.bam_CNVs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/sample_woc.bam_CNVs Sat Nov 13 18:28:40 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +M 410 15619 1 loss |