Mercurial > repos > iuc > samtools_view
diff samtools_view.xml @ 14:5826298f6a73 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e
author | iuc |
---|---|
date | Mon, 15 Aug 2022 09:19:43 +0000 |
parents | 0dbf49c414ae |
children | 6be888be75f9 |
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--- a/samtools_view.xml Sun Dec 19 15:58:19 2021 +0000 +++ b/samtools_view.xml Mon Aug 15 09:19:43 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> +<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>- reformat, filter, or subsample SAM, BAM or CRAM</description> <macros> <import>macros.xml</import> @@ -154,11 +154,11 @@ ## not dealing with all of the reads in the indexed ## file. We have to do an extra pass over the input to ## count the reads to subsample. - sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {frac=s/${mode.subsample_config.subsampling_mode.target}; print(frac > 1 ? $seed+1/frac : ".0")}'` && + sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` && #else: ## We can get the count of reads to subsample using ## an inexpensive call to idxstats. - sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=s/${mode.subsample_config.subsampling_mode.target}; print(frac > 1 ? $seed+1/frac : ".0")}'` && + sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` && #end if #end if #end if @@ -690,7 +690,7 @@ </conditional> <output name="outputsam" file="test_20.bam" ftype="bam" lines_diff="4" /> </test> - <!-- 21) sampling options--> + <!-- 21) sampling options target < total reads --> <test> <param name="input" value="in_test_15.sam" ftype="sam" /> <conditional name="mode"> @@ -707,9 +707,9 @@ </conditional> </conditional> </conditional> - <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="6" /> + <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="10" /> </test> - <!-- 22) --> + <!-- 22) target > total reads --> <test> <param name="input" value="in_test_15.sam" ftype="sam" /> <conditional name="mode"> @@ -786,7 +786,7 @@ </conditional> </conditional> </conditional> - <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="6" /> + <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="2" /> </test> <!-- 26) --> <test>