| Previous changeset 3:5f8e69cc4c6e (2020-05-16) Next changeset 5:30a201c9c310 (2024-07-11) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e5a96dae9473c2083a2312d1d00b1e55c27e1620" |
|
modified:
qualimap_bamqc.xml |
| b |
| diff -r 5f8e69cc4c6e -r 19ece8afbaab qualimap_bamqc.xml --- a/qualimap_bamqc.xml Sat May 16 09:47:55 2020 -0400 +++ b/qualimap_bamqc.xml Wed May 20 15:56:11 2020 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy2"> +<tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy3"> <macros> <import>qualimap_macros.xml</import> </macros> @@ -40,7 +40,7 @@ #end if #end if - #set input_name = re.sub('[^\s\w\-]', '_', str($input1.name)) + #set input_name = re.sub('[^\w]', '_', str($input1.element_identifier)) ln -s '$input1' '$input_name' && qualimap bamqc @@ -132,6 +132,9 @@ <data name="coverage_histogram" format="tsv" from_work_dir="results/coverage_histogram.txt" /> <data name="genome_fraction_coverage" format="tsv" from_work_dir="results/genome_fraction_coverage.txt" /> <data name="duplication_rate_histogram" format="tsv" from_work_dir="results/duplication_rate_histogram.txt" /> + <data name="homopolymer_indels" format="tsv" from_work_dir="results/homopolymer_indels.txt" /> + <data name="insert_size_across_reference" format="tsv" from_work_dir="results/insert_size_across_reference.txt" /> + <data name="insert_size_histogram" format="tsv" from_work_dir="results/insert_size_histogram.txt" /> <data name="mapped_reads_clipping_profile" format="tsv" from_work_dir="results/mapped_reads_clipping_profile.txt" /> <data name="mapped_reads_gc-content_distribution" format="tsv" from_work_dir="results/mapped_reads_gc-content_distribution.txt" /> <data name="mapped_reads_nucleotide_content" format="tsv" from_work_dir="results/mapped_reads_nucleotide_content.txt" /> @@ -140,7 +143,7 @@ </collection> </outputs> <tests> - <test expect_num_outputs="12"> + <test expect_num_outputs="15"> <param name="input1" value="test_mapped_reads.bam"/> <output name="output_html" ftype="html"> <assert_contents> @@ -151,7 +154,7 @@ <element name="genome_results" file="genome_results_default.txt" ftype="txt" compare="diff" lines_diff="2" /> </output_collection> </test> - <test expect_num_outputs="13"> + <test expect_num_outputs="16"> <param name="input1" value="test_mapped_reads.bam" /> <param name="per_base_coverage" value="true" /> <output name="output_html" ftype="html"> @@ -164,7 +167,7 @@ <element name="genome_results" file="genome_results_default.txt" ftype="txt" compare="diff" lines_diff="2" /> </output_collection> </test> - <test expect_num_outputs="12"> + <test expect_num_outputs="15"> <param name="input1" value="test_mapped_reads.bam"/> <conditional name="stats_regions"> <param name="region_select" value="custom_regions" /> @@ -179,7 +182,7 @@ <element name="genome_results" file="genome_results_inside_features.txt" ftype="txt" compare="diff" lines_diff="2" /> </output_collection> </test> - <test expect_num_outputs="13"> + <test expect_num_outputs="16"> <param name="input1" value="test_mapped_reads.bam" /> <conditional name="stats_regions"> <param name="region_select" value="custom_regions" /> @@ -196,7 +199,7 @@ <element name="genome_results" file="genome_results_inside_features.txt" ftype="txt" compare="diff" lines_diff="2" /> </output_collection> </test> - <test expect_num_outputs="13"> + <test expect_num_outputs="16"> <param name="input1" value="test_mapped_reads.bam" /> <conditional name="stats_regions"> <param name="region_select" value="custom_regions" /> @@ -469,7 +472,7 @@ The *genome_results* dataset provides a plain-text summary of key statistics, most of which can also be found in the *Summary* section of the *HTML Report*. -The remaining 9 datasets hold the tabular raw data underlying the plots of the corresponding names in the *HTML Report*. +The remaining 12 datasets hold the tabular raw data underlying the plots of the corresponding names in the *HTML Report*. Per-base coverage |