| Previous changeset 0:8db56d2f8b72 (2018-06-21) Next changeset 2:2cf36d9ea571 (2018-07-16) |
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Commit message:
planemo upload commit 9a3aeb2c588f9f67824ea5568923ce70b048499a |
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modified:
umi-tools_counts.xml |
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added:
test-data/fc.ENSDARG00000019692.bam test-data/fc.ENSDARG00000019692.counts |
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| diff -r 8db56d2f8b72 -r 3c932ad4a174 test-data/fc.ENSDARG00000019692.bam |
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| Binary file test-data/fc.ENSDARG00000019692.bam has changed |
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| diff -r 8db56d2f8b72 -r 3c932ad4a174 test-data/fc.ENSDARG00000019692.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fc.ENSDARG00000019692.counts Sat Jul 14 06:14:24 2018 -0400 |
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| @@ -0,0 +1,2 @@ +gene ACCAGA ACGTTG ACTCTG AGACAG AGTGTC ATGTCG CTAGGA GAAGAC GGTAAC TGGTGA +ENSDARG00000019692 2 1 1 1 1 1 1 1 2 1 |
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| diff -r 8db56d2f8b72 -r 3c932ad4a174 umi-tools_counts.xml --- a/umi-tools_counts.xml Thu Jun 21 15:20:14 2018 -0400 +++ b/umi-tools_counts.xml Sat Jul 14 06:14:24 2018 -0400 |
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| b'@@ -1,5 +1,5 @@\n-<tool id="umi_tools_count" name="UMI-tools count" version="@VERSION@.0">\n- <description>Count UMIs from BAM files</description>\n+<tool id="umi_tools_count" name="UMI-tools count" version="@VERSION@.1">\n+ <description>performs quantification of UMIs from BAM files</description>\n <macros>\n <import>macros.xml</import>\n <xml name="sanitize_tag" >\n@@ -10,93 +10,84 @@\n </macros>\n <expand macro="requirements" />\n <command detect_errors="exit_code"><![CDATA[\n-\n ln -s \'${input_bam}\' \'input.bam\' &&\n ln -s \'${input_bam.metadata.bam_index}\' \'input.bam.bai\' &&\n- \n+\n umi_tools count\n- -I input.bam\n- \'$bam_paired\'\n- --extract-umi-method=\'$barcodes.extract_umi_method.value\'\n- #if $barcodes.extract_umi_method == \'read_id\':\n- --umi-separator=\'$barcodes.delimiter\'\n- #else if $barcodes.extract_umi_method == \'tag\':\n- --umi-tag=\'$barcodes.umi_tag\'\n- --cell-tag=\'$barcodes.cell_tag\'\n- #end if\n- --method=\'$grouping_method.value\'\n- --edit-distance-threshold=\'$hamming_distance\'\n- --mapping-quality=\'$advanced.mapping_quality\'\n- --per-gene\n- $wide_format_cell_counts\n- $advanced.per_contig\n- \'$advanced.per_cell\'\n- #if $advanced.gene_tag:\n- --gene-tag=\'$advanced.gene_tag\'\n- #end if\n- #if $advanced.skip_tags_regex.value:\n- --skip-tags-regex=\'$advanced.skip_tags_regex\'\n- #end if\n- #if $advanced.random_seed != 0:\n+ -I input.bam\n+ \'$paired\'\n+ --extract-umi-method=\'$barcodes.extract_umi_method.value\'\n+ #if str($barcodes.extract_umi_method) == \'read_id\':\n+ --umi-separator=\'$barcodes.umi_separator.value\'\n+ #else if str($barcodes.extract_umi_method) == \'tag\':\n+ --umi-tag=\'$barcodes.umi_tag.value\'\n+ --cell-tag=\'$barcodes.cell_tag.value\'\n+ #end if\n+ --method=\'$method.value\'\n+ --edit-distance-threshold=\'$edit_distance_threshold\'\n+ --mapping-quality=\'$advanced.mapping_quality\'\n+ --per-gene\n+ \'$wide_format_cell_counts\'\n+ \'$advanced.per_contig\'\n+ \'$advanced.per_cell\'\n+ #if str($advanced.gene_tag) != "":\n+ --gene-tag=\'$advanced.gene_tag.value\'\n+ #end if\n+ #if str($advanced.skip_tags_regex) != "":\n+ --skip-tags-regex=\'$advanced.skip_tags_regex.value\'\n+ #end if\n+ #if \'$advanced.random_seed\' != 0:\n --random-seed=\'$advanced.random_seed\'\n- #end if\n- -S \'$out_counts\'\n- -L \'$out_log\'\n+ #end if\n+ -S \'$out_counts\'\n ]]></command>\n <inputs>\n <param name="input_bam" type="data" format="bam" label="Sorted BAM file" help="Please use the samtools sort tool to ensure a correct BAM input" />\n-\n- <param name="bam_paired" type="boolean" truevalue="--paired" falsevalue="" checked="false"\n- label="Bam is paired-end"\n- help="both read pairs will be output. This will also force the use of the template length to determine \n-reads with the same mapping coordinates." />\n-\n+ <param argument="--paired" type="boolean" truevalue="--paired" falsevalue="" checked="false" label="Bam is paired-end" help="both read pairs will be output. This will also force the use of the template length to determine reads with the same mapping coordinates." />\n <conditional name="barcodes" >\n- <param name="extract_umi_method" type="select" label="Umi Extract Method" help="How are the barcodes encoded in the read?" >\n+ <param argument="--extract-umi-method" name="extract_umi_method" type="select" label="Umi Extract Method" help="How are the barcodes encoded in the read?" >\n <option value="read_id" selected="true">Barcodes are contained at the end of the read seperated by '..b'NAME)"\n- help="All reads with the same contig will be considered to have the same alignment position. This is useful if you have aligned to a reference transcriptome with one transcript per gene." />\n- <param name="per_cell" type="boolean" truevalue="--per-cell" falsevalue="" checked="false"\n- label="Group reads only if they have the same cell barcode." />\n- <param name="random_seed" type="integer" min="0" value="0" label="Random Seed" />\n- </section> \n+ <param argument="--per-contig" name="per_contig" type="boolean" truevalue="--per-contig" falsevalue="" checked="false" label="Deduplicate per contig (field 3 in BAM; RNAME)" help="All reads with the same contig will be considered to have the same alignment position. This is useful if you have aligned to a reference transcriptome with one transcript per gene." />\n+ <param argument="--per-cell" name="per_cell" type="boolean" truevalue="--per-cell" falsevalue="" checked="true" label="Group reads only if they have the same cell barcode." />\n+ <param argument="--random-seed" name="random_seed" type="integer" min="0" value="0" label="Random Seed" />\n+ </section>\n </inputs>\n <outputs>\n- <data name="out_counts" format="tsv" />\n- <data name="out_log" format="txt" />\n+ <data name="out_counts" format="tabular" />\n </outputs>\n <tests>\n <test><!--count_single_gene_tag:-->\n <param name="input_bam" value="chr19_gene_tags.bam" />\n <param name="random_seed" value="123456789" />\n- <param name="grouping_method" value="directional" />\n+ <param name="method" value="directional" />\n <param name="gene_tag" value="XF" />\n <param name="skip_tags_regex" value="^[__|Unassigned]" />\n <param name="extract_umi_method" value="umis" />\n+ <param name="wide_format_cell_counts" value="false" />\n+ <param name="per_cell" value="false" />\n <output name="out_counts" value="count_single_gene_tag.tsv" />\n </test>\n <test><!--count_single_cells_gene_tag:-->\n <param name="input_bam" value="chr19_gene_tags.bam" />\n <param name="random_seed" value="123456789" />\n- <param name="grouping_method" value="directional" />\n+ <param name="method" value="directional" />\n <param name="gene_tag" value="XF" />\n <param name="skip_tags_regex" value="^[__|Unassigned]" />\n- <param name="per_cell" value="true" /><!-- new -->\n+ <param name="per_cell" value="true" />\n <param name="extract_umi_method" value="umis" />\n+ <param name="wide_format_cell_counts" value="false" />\n <output name="out_counts" value="count_single_cells_gene_tag.tsv" />\n </test>\n <test><!--count_single_cells_wide_gene_tag:-->\n <param name="input_bam" value="chr19_gene_tags.bam" />\n <param name="random_seed" value="123456789" />\n- <param name="grouping_method" value="directional" />\n+ <param name="method" value="directional" />\n <param name="gene_tag" value="XF" />\n <param name="skip_tags_regex" value="^[__|Unassigned]" />\n- <param name="per_cell" value="true" /><!-- new -->\n+ <param name="per_cell" value="true" />\n <param name="extract_umi_method" value="umis" />\n <param name="wide_format_cell_counts" value="true" />\n <output name="out_counts" value="count_single_cells_gene_tag_wide.tsv" />\n </test>\n+ <test><!-- count ENSDARG00000019692, with defaults -->\n+ <param name="input_bam" value="fc.ENSDARG00000019692.bam" />\n+ <param name="method" value="unique" />\n+ <output name="out_counts" value="fc.ENSDARG00000019692.counts" />\n+ </test>\n </tests>\n <help><![CDATA[\n \n' |