Mercurial > repos > iuc > metabat2_jgi_summarize_bam_contig_depths
changeset 4:00e3b4ef7e0c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 37e664b4211a39ac3dba2adb871c0b0ec80a4215
| author | iuc |
|---|---|
| date | Sat, 25 Jan 2025 21:16:23 +0000 |
| parents | ec045ca00b50 |
| children | |
| files | jgi_summarize_bam_contig_depths.xml macros.xml test-data/jgi_output1.tabular test-data/jgi_output2.tabular test-data/jgi_output_depth1.tabular |
| diffstat | 5 files changed, 36 insertions(+), 12 deletions(-) [+] |
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--- a/jgi_summarize_bam_contig_depths.xml Thu Nov 09 12:24:01 2023 +0000 +++ b/jgi_summarize_bam_contig_depths.xml Sat Jan 25 21:16:23 2025 +0000 @@ -152,7 +152,15 @@ <param name="type" value="individual"/> <param name="bam_indiv_input" value="input1.bam" ftype="bam"/> </conditional> - <output name="outputDepth" file="jgi_output1.tabular" ftype="tabular" compare="contains"/> + <output name="outputDepth" ftype="tabular"> + <assert_contents> + <has_n_lines n="2"/> + <has_n_columns n="5"/> + <has_text text="50.6321"/> + <has_text text="16569"/> + <has_text text="gi|251831106|ref|NC_012920.1|"/> + </assert_contents> + </output> </test> <!-- Multiple inputs, default settings --> <test expect_num_outputs="1"> @@ -160,7 +168,14 @@ <param name="type" value="co"/> <param name="bam_co_inputs" value="input1.bam,input1.bam" ftype="bam"/> </conditional> - <output name="outputDepth" file="jgi_output2.tabular" ftype="tabular" compare="contains"/> + <output name="outputDepth" ftype="tabular"> + <assert_contents> + <has_n_lines n="2"/> + <has_n_columns n="7"/> + <has_text text="16569"/> + <has_text text="gi|251831106|ref|NC_012920.1|"/> + </assert_contents> + </output> </test> <!-- Single input, output paired contigs, reference from history --> <test expect_num_outputs="5"> @@ -178,7 +193,14 @@ <section name="advanced"> <param name="output_paired_contigs" value="true"/> </section> - <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/> + <output name="outputDepth" ftype="tabular"> + <assert_contents> + <has_n_lines n="2"/> + <has_n_columns n="5"/> + <has_text text="7000"/> + <has_text text="NC_002945.4"/> + </assert_contents> + </output> <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/> <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/> <output name="outputReadStats" file="jgi_output_read_stats1.tabular" ftype="tabular"/> @@ -199,7 +221,14 @@ <section name="advanced"> <param name="output_paired_contigs" value="true"/> </section> - <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/> + <output name="outputDepth" ftype="tabular"> + <assert_contents> + <has_n_lines n="2"/> + <has_n_columns n="5"/> + <has_text text="7000"/> + <has_text text="NC_002945.4"/> + </assert_contents> + </output> <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/> <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/> <output name="outputReadStats" file="jgi_output_read_stats1.tabular" ftype="tabular"/> @@ -207,6 +236,7 @@ </test> </tests> <help><![CDATA[ + **What it does** Calculates coverage depth for each sequence in one or more selected BAM files, producing a tabular file (for each input)
--- a/macros.xml Thu Nov 09 12:24:01 2023 +0000 +++ b/macros.xml Sat Jan 25 21:16:23 2025 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">2.15</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@TOOL_VERSION@">2.17</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.01</token> <xml name="biotools"> <xrefs>
--- a/test-data/jgi_output1.tabular Thu Nov 09 12:24:01 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -contigName contigLen totalAvgDepth -gi|251831106|ref|NC_012920.1| 16569 0.667885 0.667885 50.6321