Mercurial > repos > iuc > qualimap_bamqc
comparison qualimap_bamqc.xml @ 4:19ece8afbaab draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e5a96dae9473c2083a2312d1d00b1e55c27e1620"
author | iuc |
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date | Wed, 20 May 2020 15:56:11 -0400 |
parents | 5f8e69cc4c6e |
children | 30a201c9c310 |
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3:5f8e69cc4c6e | 4:19ece8afbaab |
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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 |