Mercurial > repos > iuc > qualimap_bamqc

comparison qualimap_bamqc.xml @ 4:19ece8afbaab draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e5a96dae9473c2083a2312d1d00b1e55c27e1620"
author iuc
date Wed, 20 May 2020 15:56:11 -0400
parents 5f8e69cc4c6e
children 30a201c9c310
comparison
equal deleted inserted replaced
3:5f8e69cc4c6e 4:19ece8afbaab
1 <tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy2"> 1 <tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy3">
2 <macros> 2 <macros>
3 <import>qualimap_macros.xml</import> 3 <import>qualimap_macros.xml</import>
4 </macros> 4 </macros>
5 <expand macro="requirements" /> 5 <expand macro="requirements" />
6 <expand macro="version_command" /> 6 <expand macro="version_command" />
38 #set $per_base_coverage_target = '/dev/null' 38 #set $per_base_coverage_target = '/dev/null'
39 #end if 39 #end if
40 #end if 40 #end if
41 #end if 41 #end if
42 42
43 #set input_name = re.sub('[^\s\w\-]', '_', str($input1.name)) 43 #set input_name = re.sub('[^\w]', '_', str($input1.element_identifier))
44 ln -s '$input1' '$input_name' && 44 ln -s '$input1' '$input_name' &&
45 45
46 qualimap bamqc 46 qualimap bamqc
47 -bam '$input_name' -outdir results -outformat html 47 -bam '$input_name' -outdir results -outformat html
48 --collect-overlap-pairs 48 --collect-overlap-pairs
130 <data name="genome_results" format="txt" from_work_dir="results/summary_report.txt" /> 130 <data name="genome_results" format="txt" from_work_dir="results/summary_report.txt" />
131 <data name="coverage_across_reference" format="tsv" from_work_dir="results/coverage_across_reference.txt" /> 131 <data name="coverage_across_reference" format="tsv" from_work_dir="results/coverage_across_reference.txt" />
132 <data name="coverage_histogram" format="tsv" from_work_dir="results/coverage_histogram.txt" /> 132 <data name="coverage_histogram" format="tsv" from_work_dir="results/coverage_histogram.txt" />
133 <data name="genome_fraction_coverage" format="tsv" from_work_dir="results/genome_fraction_coverage.txt" /> 133 <data name="genome_fraction_coverage" format="tsv" from_work_dir="results/genome_fraction_coverage.txt" />
134 <data name="duplication_rate_histogram" format="tsv" from_work_dir="results/duplication_rate_histogram.txt" /> 134 <data name="duplication_rate_histogram" format="tsv" from_work_dir="results/duplication_rate_histogram.txt" />
135 <data name="homopolymer_indels" format="tsv" from_work_dir="results/homopolymer_indels.txt" />
136 <data name="insert_size_across_reference" format="tsv" from_work_dir="results/insert_size_across_reference.txt" />
137 <data name="insert_size_histogram" format="tsv" from_work_dir="results/insert_size_histogram.txt" />
135 <data name="mapped_reads_clipping_profile" format="tsv" from_work_dir="results/mapped_reads_clipping_profile.txt" /> 138 <data name="mapped_reads_clipping_profile" format="tsv" from_work_dir="results/mapped_reads_clipping_profile.txt" />
136 <data name="mapped_reads_gc-content_distribution" format="tsv" from_work_dir="results/mapped_reads_gc-content_distribution.txt" /> 139 <data name="mapped_reads_gc-content_distribution" format="tsv" from_work_dir="results/mapped_reads_gc-content_distribution.txt" />
137 <data name="mapped_reads_nucleotide_content" format="tsv" from_work_dir="results/mapped_reads_nucleotide_content.txt" /> 140 <data name="mapped_reads_nucleotide_content" format="tsv" from_work_dir="results/mapped_reads_nucleotide_content.txt" />
138 <data name="mapping_quality_across_reference" format="tsv" from_work_dir="results/mapping_quality_across_reference.txt" /> 141 <data name="mapping_quality_across_reference" format="tsv" from_work_dir="results/mapping_quality_across_reference.txt" />
139 <data name="mapping_quality_histogram" format="tsv" from_work_dir="results/mapping_quality_histogram.txt" /> 142 <data name="mapping_quality_histogram" format="tsv" from_work_dir="results/mapping_quality_histogram.txt" />
140 </collection> 143 </collection>
141 </outputs> 144 </outputs>
142 <tests> 145 <tests>
143 <test expect_num_outputs="12"> 146 <test expect_num_outputs="15">
144 <param name="input1" value="test_mapped_reads.bam"/> 147 <param name="input1" value="test_mapped_reads.bam"/>
145 <output name="output_html" ftype="html"> 148 <output name="output_html" ftype="html">
146 <assert_contents> 149 <assert_contents>
147 <has_text text="Qualimap report: BAM QC" /> 150 <has_text text="Qualimap report: BAM QC" />
148 </assert_contents> 151 </assert_contents>
149 </output> 152 </output>
150 <output_collection name="raw_data" type="list"> 153 <output_collection name="raw_data" type="list">
151 <element name="genome_results" file="genome_results_default.txt" ftype="txt" compare="diff" lines_diff="2" /> 154 <element name="genome_results" file="genome_results_default.txt" ftype="txt" compare="diff" lines_diff="2" />
152 </output_collection> 155 </output_collection>
153 </test> 156 </test>
154 <test expect_num_outputs="13"> 157 <test expect_num_outputs="16">
155 <param name="input1" value="test_mapped_reads.bam" /> 158 <param name="input1" value="test_mapped_reads.bam" />
156 <param name="per_base_coverage" value="true" /> 159 <param name="per_base_coverage" value="true" />
157 <output name="output_html" ftype="html"> 160 <output name="output_html" ftype="html">
158 <assert_contents> 161 <assert_contents>
159 <has_text text="Qualimap report: BAM QC" /> 162 <has_text text="Qualimap report: BAM QC" />
162 <output name="output_per_base_coverage" file="per_base_coverage_default.txt" ftype="tsv" /> 165 <output name="output_per_base_coverage" file="per_base_coverage_default.txt" ftype="tsv" />
163 <output_collection name="raw_data" type="list"> 166 <output_collection name="raw_data" type="list">
164 <element name="genome_results" file="genome_results_default.txt" ftype="txt" compare="diff" lines_diff="2" /> 167 <element name="genome_results" file="genome_results_default.txt" ftype="txt" compare="diff" lines_diff="2" />
165 </output_collection> 168 </output_collection>
166 </test> 169 </test>
167 <test expect_num_outputs="12"> 170 <test expect_num_outputs="15">
168 <param name="input1" value="test_mapped_reads.bam"/> 171 <param name="input1" value="test_mapped_reads.bam"/>
169 <conditional name="stats_regions"> 172 <conditional name="stats_regions">
170 <param name="region_select" value="custom_regions" /> 173 <param name="region_select" value="custom_regions" />
171 <param name="regions" value="features.gtf" /> 174 <param name="regions" value="features.gtf" />
172 </conditional> 175 </conditional>
177 </output> 180 </output>
178 <output_collection name="raw_data" type="list"> 181 <output_collection name="raw_data" type="list">
179 <element name="genome_results" file="genome_results_inside_features.txt" ftype="txt" compare="diff" lines_diff="2" /> 182 <element name="genome_results" file="genome_results_inside_features.txt" ftype="txt" compare="diff" lines_diff="2" />
180 </output_collection> 183 </output_collection>
181 </test> 184 </test>
182 <test expect_num_outputs="13"> 185 <test expect_num_outputs="16">
183 <param name="input1" value="test_mapped_reads.bam" /> 186 <param name="input1" value="test_mapped_reads.bam" />
184 <conditional name="stats_regions"> 187 <conditional name="stats_regions">
185 <param name="region_select" value="custom_regions" /> 188 <param name="region_select" value="custom_regions" />
186 <param name="regions" value="features.gtf" /> 189 <param name="regions" value="features.gtf" />
187 </conditional> 190 </conditional>
194 <output name="output_per_base_coverage" file="per_base_coverage_inside_features.txt" ftype="tsv" /> 197 <output name="output_per_base_coverage" file="per_base_coverage_inside_features.txt" ftype="tsv" />
195 <output_collection name="raw_data" type="list"> 198 <output_collection name="raw_data" type="list">
196 <element name="genome_results" file="genome_results_inside_features.txt" ftype="txt" compare="diff" lines_diff="2" /> 199 <element name="genome_results" file="genome_results_inside_features.txt" ftype="txt" compare="diff" lines_diff="2" />
197 </output_collection> 200 </output_collection>
198 </test> 201 </test>
199 <test expect_num_outputs="13"> 202 <test expect_num_outputs="16">
200 <param name="input1" value="test_mapped_reads.bam" /> 203 <param name="input1" value="test_mapped_reads.bam" />
201 <conditional name="stats_regions"> 204 <conditional name="stats_regions">
202 <param name="region_select" value="custom_regions" /> 205 <param name="region_select" value="custom_regions" />
203 <param name="regions" value="features.gtf" /> 206 <param name="regions" value="features.gtf" />
204 <param name="outside_stats" value="true" /> 207 <param name="outside_stats" value="true" />
467 This is a *Collection* of 10 individual datasets. 470 This is a *Collection* of 10 individual datasets.
468 471
469 The *genome_results* dataset provides a plain-text summary of key statistics, 472 The *genome_results* dataset provides a plain-text summary of key statistics,
470 most of which can also be found in the *Summary* section of the *HTML Report*. 473 most of which can also be found in the *Summary* section of the *HTML Report*.
471 474
472 The remaining 9 datasets hold the tabular raw data underlying the plots of the corresponding names in the *HTML Report*. 475 The remaining 12 datasets hold the tabular raw data underlying the plots of the corresponding names in the *HTML Report*.
473 476
474 477
475 Per-base coverage 478 Per-base coverage
476 ----------------- 479 -----------------
477 480