| Previous changeset 6:d04d9f1c6791 (2015-04-21) Next changeset 8:f7a0d41036c7 (2017-05-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/sam_to_bam commit a1517c9d22029095120643bbe2c8fa53754dd2b7 |
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modified:
sam_to_bam.xml tool_dependencies.xml |
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added:
test-data/sam_to_bam_noheader_in2.sam test-data/sam_to_bam_out3.bam |
| b |
| diff -r d04d9f1c6791 -r 881e16ad05c6 sam_to_bam.xml --- a/sam_to_bam.xml Tue Apr 21 14:52:20 2015 -0400 +++ b/sam_to_bam.xml Wed Nov 11 12:51:52 2015 -0500 |
| [ |
| @@ -1,22 +1,21 @@ -<tool id="sam_to_bam" name="SAM-to-BAM" version="2.0"> +<tool id="sam_to_bam" name="SAM-to-BAM" version="2.1"> <description>convert SAM to BAM</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"></expand> + <expand macro="stdio"></expand> <expand macro="version_command"></expand> - <expand macro="stdio"></expand> <command> <![CDATA[ - samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o sorted_input.bam -T temp "$input1" && - #if $source.index_source == "history": - ln -s $source.ref_file input.fa && - samtools faidx input.fa && - #else - ln -s ${source.index.fields.path} input.fa && - ln -s ${source.index.fields.path}.fai input.fa.fai && - #end if - samtools view -@ \${GALAXY_SLOTS:-1} -b -h -o $output1 -T input.fa sorted_input.bam + #if $source.index_source == "history": + ln -s $source.ref_file input.fa && + samtools faidx input.fa && + #else + ln -s ${source.index.fields.path} input.fa && + ln -s ${source.index.fields.path}.fai input.fa.fai && + #end if + samtools view -b -@ \${GALAXY_SLOTS:-1} -t input.fa.fai "$input1" | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o "$output1" -T temp ]]> </command> <inputs> @@ -68,6 +67,12 @@ <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" /> <output file="sam_to_bam_out1.bam" ftype="bam" name="output1" /> </test> + <test> + <param name="index_source" value="history" /> + <param name="input1" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> + <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" /> + <output file="sam_to_bam_out3.bam" ftype="bam" name="output1" /> + </test> </tests> <help> <![CDATA[ |
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| diff -r d04d9f1c6791 -r 881e16ad05c6 test-data/sam_to_bam_noheader_in2.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sam_to_bam_noheader_in2.sam Wed Nov 11 12:51:52 2015 -0500 |
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| @@ -0,0 +1,10 @@ +HWI-EAS91_1_30788AAXX:1:1:1513:715 16 chrM 9563 25 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1698:516 16 chrM 2735 25 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1491:637 16 chrM 10864 25 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1711:249 16 chrM 10617 25 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1634:211 0 chrM 9350 25 36M * 0 0 GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1218:141 16 chrM 14062 25 36M * 0 0 ACAAAACTAACAACAAAAATAACACTCNNAATAAAC I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1398:854 16 chrM 3921 25 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1310:991 16 chrM 10002 25 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTANNACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1716:413 0 chrM 6040 25 36M * 0 0 GATCCAANNCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1630:59 16 chrM 12387 25 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 |
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| diff -r d04d9f1c6791 -r 881e16ad05c6 test-data/sam_to_bam_out3.bam |
| b |
| Binary file test-data/sam_to_bam_out3.bam has changed |
| b |
| diff -r d04d9f1c6791 -r 881e16ad05c6 tool_dependencies.xml --- a/tool_dependencies.xml Tue Apr 21 14:52:20 2015 -0400 +++ b/tool_dependencies.xml Wed Nov 11 12:51:52 2015 -0500 |
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| @@ -1,6 +1,6 @@ <?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" /> + <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |