| Previous changeset 56:daae0a118c36 (2018-09-18) Next changeset 58:1a052c827e88 (2019-11-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7d7cd4324af66710b89801a1a1c79fb8abf0d146 |
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modified:
geneBody_coverage.xml inner_distance.xml tin.xml |
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| diff -r daae0a118c36 -r f437057e46f1 geneBody_coverage.xml --- a/geneBody_coverage.xml Tue Sep 18 09:11:06 2018 -0400 +++ b/geneBody_coverage.xml Thu Sep 27 14:23:52 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@WRAPPER_VERSION@.2"> +<tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@WRAPPER_VERSION@.3"> <description> Read coverage over gene body. </description> @@ -29,9 +29,9 @@ #end for geneBody_coverage.py -i 'input_list.txt' -r '${refgene}' --minimum_length ${minimum_length} -o output #else - #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier) - ln -sf '${input}' '${safename}.bam' && - ln -sf '${input.metadata.bam_index}' '${safename}.bam.bai' && + #set $safename = re.sub('[^\w\-_]', '_', $batch_mode.input.element_identifier) + ln -sf '${batch_mode.input}' '${safename}.bam' && + ln -sf '${batch_mode.input.metadata.bam_index}' '${safename}.bam.bai' && geneBody_coverage.py -i '${safename}.bam' -r '${refgene}' --minimum_length ${minimum_length} -o output #end if ]]> |
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| diff -r daae0a118c36 -r f437057e46f1 inner_distance.xml --- a/inner_distance.xml Tue Sep 18 09:11:06 2018 -0400 +++ b/inner_distance.xml Thu Sep 27 14:23:52 2018 -0400 |
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| @@ -88,7 +88,7 @@ 1. output.inner_distance.txt: - first column is read ID - -second column is inner distance. Could be negative value if PE reads were overlapped or mapping error (e.g. Read1_start < Read2_start, while Read1_end >> Read2_end due to spliced mapping of read1) + - second column is inner distance. Could be negative value if PE reads were overlapped or mapping error (e.g. Read1_start < Read2_start, while Read1_end >> Read2_end due to spliced mapping of read1) - third column indicates how paired reads were mapped: PE_within_same_exon, PE_within_diff_exon,PE_reads_overlap 2. output..inner_distance_freq.txt: - inner distance starts |
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| diff -r daae0a118c36 -r f437057e46f1 tin.xml --- a/tin.xml Tue Sep 18 09:11:06 2018 -0400 +++ b/tin.xml Thu Sep 27 14:23:52 2018 -0400 |
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| @@ -89,7 +89,7 @@ * RIN has very limited sensitivity to measure substantially degraded RNA samples such as preserved clinical tissues. (ref: - http://www.illumina.com/documents/products/technotes/technote-truseq-rna-access.pdf). + https://www.illumina.com/content/dam/illumina-marketing/documents/products/technotes/technote-truseq-rna-access.pdf). To overcome these limitations, we developed TIN, an algorithm that is able to measure RNA integrity at transcript level. TIN calculates a score (0 <= |