| Previous changeset 2:0072bf593791 (2015-04-21) Next changeset 4:4e404acfafa6 (2018-09-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 |
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modified:
macros.xml samtools_flagstat.xml test-data/samtools_flagstat_out1.txt |
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removed:
tool_dependencies.xml |
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| diff -r 0072bf593791 -r cc61ade70eb8 macros.xml --- a/macros.xml Tue Apr 21 15:56:53 2015 -0400 +++ b/macros.xml Tue May 09 11:18:29 2017 -0400 |
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| @@ -1,16 +1,17 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="1.3.1">samtools</requirement> <yield/> </requirements> </xml> + <token name="@TOOL_VERSION@">1.3.1</token> <xml name="citations"> <citations> <citation type="bibtex"> @misc{SAM_def, title={Definition of SAM/BAM format}, - url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + url = {https://samtools.github.io/hts-specs/},} </citation> <citation type="doi">10.1093/bioinformatics/btp352</citation> <citation type="doi">10.1093/bioinformatics/btr076</citation> @@ -41,7 +42,7 @@ </citations> </xml> <xml name="version_command"> - <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> </xml> <xml name="stdio"> <stdio> @@ -64,7 +65,5 @@ 5. Click **Save** The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. - </token> - </macros> |
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| diff -r 0072bf593791 -r cc61ade70eb8 samtools_flagstat.xml --- a/samtools_flagstat.xml Tue Apr 21 15:56:53 2015 -0400 +++ b/samtools_flagstat.xml Tue May 09 11:18:29 2017 -0400 |
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| @@ -1,32 +1,37 @@ -<tool id="samtools_flagstat" name="Flagstat" version="2.0"> - <description>tabulate descriptive stats for BAM datset</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio"></expand> - <expand macro="version_command"></expand> - <command>samtools flagstat "$input1" > "$output1" - </command> - <inputs> - <param name="input1" type="data" format="bam" label="BAM File to Convert" /> - </inputs> - <outputs> - <data name="output1" format="txt" /> - </outputs> - <tests> - <test> - <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" /> - <output name="output1" file="samtools_flagstat_out1.txt" /> - </test> - </tests> - <help> +<tool id="samtools_flagstat" name="Flagstat" version="2.0.1"> + <description>tabulate descriptive stats for BAM datset</description> + + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + + <command><![CDATA[ + samtools flagstat '$input1' > '$output1' + ]]></command> + <inputs> + <param name="input1" type="data" format="bam" label="BAM File to report statistics of" /> + </inputs> + + <outputs> + <data name="output1" format="txt" /> + </outputs> + + <tests> + <test> + <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" /> + <output name="output1" file="samtools_flagstat_out1.txt" /> + </test> + </tests> + <help><![CDATA[ **What it does** Uses ``samtools flagstat`` command to print descriptive information for a BAM dataset. Here is an example of such information:: - 200 + 0 in total (QC-passed reads + QC-failed reads) + 200 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates @@ -39,7 +44,6 @@ 25 + 0 singletons (12.50%:nan%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) - - </help> - <expand macro="citations"></expand> + ]]></help> + <expand macro="citations"/> </tool> |
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| diff -r 0072bf593791 -r cc61ade70eb8 test-data/samtools_flagstat_out1.txt --- a/test-data/samtools_flagstat_out1.txt Tue Apr 21 15:56:53 2015 -0400 +++ b/test-data/samtools_flagstat_out1.txt Tue May 09 11:18:29 2017 -0400 |
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| @@ -2,12 +2,12 @@ 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates -25 + 0 mapped (12.50%:nan%) +25 + 0 mapped (12.50% : N/A) 200 + 0 paired in sequencing 100 + 0 read1 100 + 0 read2 -0 + 0 properly paired (0.00%:nan%) +0 + 0 properly paired (0.00% : N/A) 0 + 0 with itself and mate mapped -25 + 0 singletons (12.50%:nan%) +25 + 0 singletons (12.50% : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) |
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| diff -r 0072bf593791 -r cc61ade70eb8 tool_dependencies.xml --- a/tool_dependencies.xml Tue Apr 21 15:56:53 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="samtools" version="1.2"> - <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |