Mercurial > repos > iuc > umi_tools_dedup
changeset 11:7fa28eb10fed draft
"planemo upload commit 2da1197aac6a18df9252e5da096645d2ecaece88"
| author | iuc |
|---|---|
| date | Wed, 10 Feb 2021 19:30:35 +0000 |
| parents | c6567483aa1e |
| children | 4098ab380097 |
| files | test-data/stats_outputs_edit_distance.tsv test-data/stats_outputs_per_umi.tsv test-data/stats_outputs_per_umi_per_position.tsv umi-tools_dedup.xml |
| diffstat | 4 files changed, 52 insertions(+), 7 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stats_outputs_edit_distance.tsv Wed Feb 10 19:30:35 2021 +0000 @@ -0,0 +1,3 @@ +unique unique_null directional directional_null edit_distance +491 491 491 491 Single_UMI +0 0 0 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stats_outputs_per_umi.tsv Wed Feb 10 19:30:35 2021 +0000 @@ -0,0 +1,17 @@ +UMI median_counts_pre times_observed_pre total_counts_pre median_counts_post times_observed_post total_counts_post +AA 1 34 35 1 34 35 +AC 1 35 35 1 35 35 +AG 1 25 25 1 25 25 +AT 1 50 50 1 50 50 +CA 1 27 27 1 27 27 +CC 1 21 21 1 21 21 +CG 1 11 11 1 11 11 +CT 1 23 24 1 23 24 +GA 1 24 24 1 24 24 +GC 1 23 23 1 23 23 +GG 1 31 32 1 31 32 +GT 1 27 28 1 27 28 +TA 1 61 63 1 61 63 +TC 1 24 24 1 24 24 +TG 1 27 27 1 27 27 +TT 1 48 48 1 48 48
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stats_outputs_per_umi_per_position.tsv Wed Feb 10 19:30:35 2021 +0000 @@ -0,0 +1,4 @@ +counts instances_pre instances_post +1 486 486 +2 4 4 +3 1 1
--- a/umi-tools_dedup.xml Thu Dec 05 01:32:18 2019 -0500 +++ b/umi-tools_dedup.xml Wed Feb 10 19:30:35 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="umi_tools_dedup" name="UMI-tools deduplicate" version="@VERSION@.0"> +<tool id="umi_tools_dedup" name="UMI-tools deduplicate" version="@VERSION@+galaxy1"> <description>Extract UMI from fastq files</description> <macros> <import>macros.xml</import> @@ -16,6 +16,7 @@ #end if umi_tools dedup + '$output_stats_bool' --random-seed 0 --extract-umi-method $extract_umi_method #if str($extract_umi_method) != 'read_id': @@ -63,51 +64,71 @@ <param name="per_gene" argument="--per-gene" type="boolean" truevalue="--per-gene" falsevalue="" label="Deduplicate per gene" help="As above except with this option you can align to a reference transcriptome with more than one transcript per gene. You need to also provide a map of genes to transcripts. This will also add a metacontig ('MC') tag to the output BAM file." /> <param name="gene_transcript_map" argument="--gene-transcript-map" type="data" format="tabular" optional="True" label="Tabular file mapping genes to transripts" /> <param name="gene_tag" argument="--gene-tag" type="text" optional="True" label="Deduplicate by this gene tag" help="As --per-gene except here the gene information is encoded in the bam read tag specified so you do not need to supply the mapping file." /> + <param name="output_stats_bool" type="boolean" truevalue="--output-stats=stats_outputs" falsevalue="" checked="false" label="Output UMI related statistics files?"/> </inputs> <outputs> <data format="bam" name="output" /> + <collection name="output_stats" type="list" label="UMI_tools dedup stats"> + <filter>output_stats_bool</filter> + <data name="edit_distance" format="tabular" from_work_dir="stats_outputs_edit_distance.tsv"/> + <data name="per_umi" format="tabular" from_work_dir="stats_outputs_per_umi.tsv"/> + <data name="per_umi_per_position" format="tabular" from_work_dir="stats_outputs_per_umi_per_position.tsv"/> + </collection> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="input" value="group_in1.sam" ftype="sam" /> <param name="extract_umi_method" value="read_id" /> <param name="method" value="unique" /> <output name="output" file="dedup_out1.bam" ftype="bam" sort="True"/> </test> - <test> + <test expect_num_outputs="1"> <param name="input" value="group_in2.bam" ftype="bam" /> <param name="extract_umi_method" value="read_id" /> <param name="paired" value="True" /> <param name="method" value="unique" /> <output name="output" file="dedup_out2.bam" ftype="bam" sort="True" /> </test> - <test> + <test expect_num_outputs="1"> <param name="input" value="group_in3.bam" ftype="bam" /> <param name="extract_umi_method" value="read_id" /> <param name="method" value="unique" /> <output name="output" file="dedup_out3.bam" ftype="bam" sort="True" /> </test> - <test> + <test expect_num_outputs="1"> <param name="input" value="group_in4.bam" ftype="bam" /> <param name="extract_umi_method" value="tag" /> <param name="umi_tag" value="BX" /> <param name="method" value="unique" /> <output name="output" file="dedup_out4.bam" ftype="bam" sort="True" /> </test> - <test> + <test expect_num_outputs="1"> <param name="input" value="group_in5.bam" ftype="bam" /> <param name="extract_umi_method" value="read_id" /> <param name="umi_tag" value="BX" /> <param name="method" value="cluster" /> <output name="output" file="dedup_out5.bam" ftype="bam" sort="True" /> </test> - <test> + <test expect_num_outputs="1"> <param name="input" value="group_in6.bam" ftype="bam" /> <param name="extract_umi_method" value="read_id" /> <param name="umi_tag" value="BX" /> <param name="method" value="directional" /> <output name="output" file="dedup_out6.bam" ftype="bam" sort="True" /> </test> + <test expect_num_outputs="5"> + <param name="input" value="group_in6.bam" ftype="bam" /> + <param name="extract_umi_method" value="read_id" /> + <param name="umi_tag" value="BX" /> + <param name="method" value="directional" /> + <param name="output_stats_bool" value="true"/> + <output name="output" file="dedup_out6.bam" ftype="bam" sort="True" /> + <output_collection name="output_stats"> + <element name="edit_distance" file="stats_outputs_edit_distance.tsv" /> + <element name="per_umi" file="stats_outputs_per_umi.tsv" /> + <element name="per_umi_per_position" file="stats_outputs_per_umi_per_position.tsv" /> + </output_collection> + </test> </tests> <help><![CDATA[ umi_tools dedup - Deduplicate reads based on their UMI