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comparison batch.xml @ 1:0c60bd0f4de6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
author iuc
date Fri, 29 Sep 2023 15:28:46 +0000
parents 840fea8d07a3
children 0d371963d4b9
comparison
equal deleted inserted replaced
0:840fea8d07a3 1:0c60bd0f4de6
2 <description>Run the CNVkit pipeline on one or more BAM files</description> 2 <description>Run the CNVkit pipeline on one or more BAM files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/> 6 <expand macro="xrefs"/>
7 <expand macro="creators"/>
7 <expand macro="requirements"/> 8 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$CNV_reference.input_sample_file' ./tumor.bam && 10 ln -s '$CNV_reference.input_sample_file' ./tumor.bam &&
10 ln -s '$CNV_reference.input_sample_file.metadata.bam_index' ./tumor.bam.bai && 11 ln -s '$CNV_reference.input_sample_file.metadata.bam_index' ./tumor.bam.bai &&
11 #if str($CNV_reference.CNV_reference_availabel) == "yes": 12 #if str($CNV_reference.CNV_reference_availabel) == "yes":
110 <expand macro="output_section" /> 111 <expand macro="output_section" />
111 </inputs> 112 </inputs>
112 <outputs> 113 <outputs>
113 <data name="out_sample_bintest" format="tabular" label="${tool.name} on ${on_string}: Sample Bintest" from_work_dir="tumor.bintest.cns" /> 114 <data name="out_sample_bintest" format="tabular" label="${tool.name} on ${on_string}: Sample Bintest" from_work_dir="tumor.bintest.cns" />
114 <data name="out_sample_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Sample Antitarget Coverage" from_work_dir="tumor.antitargetcoverage.cnn" /> 115 <data name="out_sample_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Sample Antitarget Coverage" from_work_dir="tumor.antitargetcoverage.cnn" />
115 <data name="out_sample_call" format="tabular" label="${tool.name} on ${on_string}: rounded absolute scale copy numbers integer (not log2 ratios) " from_work_dir="tumor.call.cns" /> 116 <data name="out_sample_call" format="tabular" label="${tool.name} on ${on_string}: Rounded absolute scale copy numbers integer (not log2 ratios)" from_work_dir="tumor.call.cns" />
116 <data name="out_sample_targetcoverage_cnn" format="tabular" label="${tool.name} on ${on_string}: Sample Target Coverage" from_work_dir="tumor.targetcoverage.cnn" /> 117 <data name="out_sample_targetcoverage_cnn" format="tabular" label="${tool.name} on ${on_string}: Sample Target Coverage" from_work_dir="tumor.targetcoverage.cnn" />
117 <data name="out_sample_cns" format="tabular" label="${tool.name} on ${on_string}: CN segmentation calls" from_work_dir="tumor.cns" /> 118 <data name="out_sample_cns" format="tabular" label="${tool.name} on ${on_string}: CN segmentation calls" from_work_dir="tumor.cns" />
118 <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="tumor.cnr" /> 119 <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="tumor.cnr" />
119 <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: Capture Antitarget" from_work_dir="capture.antitarget.bed"> 120 <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: Capture Antitarget" from_work_dir="capture.antitarget.bed">
120 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter> 121 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
121 </data> 122 </data>
122 <data name="out_control_targetcoverage" format="tabular" label="${tool.name} on ${on_string}: Output Normal Sample Target Coverage" from_work_dir="normal.targetcoverage.cnn"> 123 <data name="out_control_targetcoverage" format="tabular" label="${tool.name} on ${on_string}: Normal Sample Target Coverage" from_work_dir="normal.targetcoverage.cnn">
123 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter> 124 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
124 </data> 125 </data>
125 <data name="out_control_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Output Normal Sample Antitarget Coverage" from_work_dir="normal.antitargetcoverage.cnn"> 126 <data name="out_control_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Normal Sample Antitarget Coverage" from_work_dir="normal.antitargetcoverage.cnn">
126 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter> 127 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
127 </data> 128 </data>
128 <data name="out_reference_cnn" format="tabular" label="${tool.name} on ${on_string}: Output Copy Number Reference Profile" from_work_dir="reference.cnn"> 129 <data name="out_reference_cnn" format="tabular" label="${tool.name} on ${on_string}: Copy Number Reference Profile" from_work_dir="reference.cnn">
129 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter> 130 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
130 </data> 131 </data>
131 <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: Output Capture Target" from_work_dir="capture.target.bed"> 132 <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: Capture Target" from_work_dir="capture.target.bed">
132 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter> 133 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
133 </data> 134 </data>
134 <data name="out_reference_target_bed" format="tabular" label="${tool.name} on ${on_string}: Output Reference Target" from_work_dir="reference.target-tmp.bed"> 135 <data name="out_reference_target_bed" format="tabular" label="${tool.name} on ${on_string}: Reference Target" from_work_dir="reference.target-tmp.bed">
135 <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter> 136 <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter>
136 </data> 137 </data>
137 <data name="out_reference_antitarget_bed" format="bed" label="${tool.name} on ${on_string}: Output Reference Antitarget" from_work_dir="reference.antitarget-tmp.bed"> 138 <data name="out_reference_antitarget_bed" format="bed" label="${tool.name} on ${on_string}: Reference Antitarget" from_work_dir="reference.antitarget-tmp.bed">
138 <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter> 139 <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter>
139 </data> 140 </data>
140 <data name="out_sample_diagram_pdf" format="pdf" label="${tool.name} on ${on_string}: Output Sample Diagram" from_work_dir="tumor-diagram.pdf"> 141 <data name="out_sample_diagram_pdf" format="pdf" label="${tool.name} on ${on_string}: Sample Diagram" from_work_dir="tumor-diagram.pdf">
141 <filter>output_section['diagram']</filter> 142 <filter>output_section['diagram']</filter>
142 </data> 143 </data>
143 <data name="out_sample_scatter_png" format="png" label="${tool.name} on ${on_string}: Output Sample Scatter " from_work_dir="tumor-scatter.png"> 144 <data name="out_sample_scatter_png" format="png" label="${tool.name} on ${on_string}: Sample Scatter pdf plot " from_work_dir="tumor-scatter.png">
144 <filter>output_section['scatter']</filter> 145 <filter>output_section['scatter']</filter>
145 </data> 146 </data>
146 </outputs> 147 </outputs>
147 <tests> 148 <tests>
148 <test expect_num_outputs="13"> 149 <test expect_num_outputs="13">