Mercurial > repos > iuc > control_freec

changeset 2:f923c54a17ee draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
author iuc
date Sat, 13 Nov 2021 18:28:40 +0000
parents 2c6349fb175c
children
files control_freec.xml macros.xml 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
diffstat 6 files changed, 3377 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- 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
--- a/macros.xml	Tue Aug 18 08:52:45 2020 -0400
+++ b/macros.xml	Sat Nov 13 18:28:40 2021 +0000
@@ -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&amp;4)</option>
@@ -115,7 +126,7 @@
             <param name="sex" type="select" label="Sample sex" help="&quot;XX&quot; will exclude chr Y from the analysis. &quot;XY&quot; 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">
--- /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
@@ -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
--- /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
@@ -0,0 +1,1659 @@
+Chromosome	Start	Ratio	MedianRatio	CopyNumber
+M	1	2.45225	0.489195	2
+M	11	0.999185	0.489195	2
+M	21	0.485727	0.489195	2
+M	31	0.681691	0.489195	2
+M	41	0	0.489195	2
+M	51	0.578857	0.489195	2
+M	61	0	0.489195	2
+M	71	3.1333	0.489195	2
+M	81	1.36338	0.489195	2
+M	91	1.15771	0.489195	2
+M	101	0.49757	0.489195	2
+M	111	0.519271	0.489195	2
+M	121	0	0.489195	2
+M	131	0	0.489195	2
+M	141	0	0.489195	2
+M	151	0	0.489195	2
+M	161	0	0.489195	2
+M	171	0	0.489195	2
+M	181	0	0.489195	2
+M	191	0	0.489195	2
+M	201	0	0.489195	2
+M	211	0	0.489195	2
+M	221	0	0.489195	2
+M	231	0	0.489195	2
+M	241	0	0.489195	2
+M	251	0	0.489195	2
+M	261	0	0.489195	2
+M	271	0	0.489195	2
+M	281	0	0.489195	2
+M	291	0	0.489195	2
+M	301	0	0.489195	2
+M	311	0	0.489195	2
+M	321	0	0.489195	2
+M	331	0.499592	0.489195	2
+M	341	0.979906	0.489195	2
+M	351	1.0361	0.489195	2
+M	361	1.36311	0.489195	2
+M	371	2.04064	0.489195	2
+M	381	1.46531	0.489195	2
+M	391	1.55414	0.489195	2
+M	401	1.53048	0.489195	2
+M	411	2.44976	0.485727	1
+M	421	2.93972	0.485727	1
+M	431	3.39045	0.485727	1
+M	441	3.6349	0.485727	1
+M	451	3.99674	0.485727	1
+M	461	4.37154	0.485727	1
+M	471	5.343	0.485727	1
+M	481	7.52514	0.485727	1
+M	491	29.7664	0.485727	1
+M	501	39.1663	0.485727	1
+M	511	25.2611	0.485727	1
+M	521	19.1023	0.485727	1
+M	531	34.7662	0.485727	1
+M	541	26.3712	0.485727	1
+M	551	27.6864	0.485727	1
+M	561	31.357	0.485727	1
+M	571	35.201	0.485727	1
+M	581	37.2995	0.485727	1
+M	591	36.9698	0.485727	1
+M	601	37.2995	0.485727	1
+M	611	34.6908	0.485727	1
+M	621	32.8269	0.485727	1
+M	631	30.0468	0.485727	1
+M	641	31.119	0.485727	1
+M	651	30.637	0.485727	1
+M	661	29.5892	0.485727	1
+M	671	29.0791	0.485727	1
+M	681	26.6393	0.485727	1
+M	691	25.6706	0.485727	1
+M	701	24.2175	0.485727	1
+M	711	22.0479	0.485727	1
+M	721	16.9523	0.485727	1
+M	731	13.5618	0.485727	1
+M	741	8.74308	0.485727	1
+M	751	8.40371	0.485727	1
+M	761	9.54367	0.485727	1
+M	771	9.54367	0.485727	1
+M	781	3.98056	0.485727	1
+M	791	4.37154	0.485727	1
+M	801	4.49633	0.485727	1
+M	811	4.08117	0.485727	1
+M	821	2.46466	0.485727	1
+M	831	3.11563	0.485727	1
+M	841	1.55781	0.485727	1
+M	851	0.968701	0.485727	1
+M	861	0.578857	0.485727	1
+M	871	1.36338	0.485727	1
+M	881	0.971454	0.485727	1
+M	891	2.04507	0.485727	1
+M	901	0.968701	0.485727	1
+M	911	0.999185	0.485727	1
+M	921	0.968701	0.485727	1
+M	931	0.979906	0.485727	1
+M	941	0.499592	0.485727	1
+M	951	1.0361	0.485727	1
+M	961	1.0361	0.485727	1
+M	971	0.976874	0.485727	1
+M	981	1.03854	0.485727	1
+M	991	0.976874	0.485727	1
+M	1001	0.519271	0.485727	1
+M	1011	0.510147	0.485727	1
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+M	1371	0.510159	0.485727	1
+M	1381	1.0361	0.485727	1
+M	1391	1.53048	0.485727	1
+M	1401	1.55414	0.485727	1
+M	1411	0.999185	0.485727	1
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+M	1431	0.485727	0.485727	1
+M	1441	0.681691	0.485727	1
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+M	1471	1.15771	0.485727	1
+M	1481	2.44976	0.485727	1
+M	1491	2.5508	0.485727	1
+M	1501	2.05388	0.485727	1
+M	1511	2.44219	0.485727	1
+M	1521	1.95375	0.485727	1
+M	1531	1.0361	0.485727	1
+M	1541	1.03854	0.485727	1
+M	1551	0.968701	0.485727	1
+M	1561	0.968701	0.485727	1
+M	1571	0.979906	0.485727	1
+M	1581	0.485727	0.485727	1
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+M	1661	1.5757	0.485727	1
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+M	1951	0	0.485727	1
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+M	1971	0	0.485727	1
+M	1981	0	0.485727	1
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+M	2391	0.999185	0.485727	1
+M	2401	0.499592	0.485727	1
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+M	2501	1.94291	0.485727	1
+M	2511	2.62616	0.485727	1
+M	2521	3.15139	0.485727	1
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+M	2541	4.69995	0.485727	1
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+M	2561	0.971454	0.485727	1
+M	2571	0.489953	0.485727	1
+M	2581	1.53048	0.485727	1
+M	2591	2.07709	0.485727	1
+M	2601	1.49878	0.485727	1
+M	2611	1.45305	0.485727	1
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--- /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
@@ -0,0 +1,1658 @@
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--- /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
@@ -0,0 +1,1 @@
+M	410	15619	1	loss