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comparison sam_to_bam.xml @ 12:9bd1568619cd draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
author iuc
date Sat, 27 Nov 2021 12:31:54 +0000
parents 1e69848b596f
children
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11:1e69848b596f 12:9bd1568619cd
14 @PREPARE_FASTA_IDX@ 14 @PREPARE_FASTA_IDX@
15 15
16 samtools view 16 samtools view
17 -b 17 -b
18 -@ \$addthreads 18 -@ \$addthreads
19 -t '$reffai' 19 -t "\$reffai"
20 '$input' | 20 '$input' |
21 21
22 samtools sort 22 samtools sort
23 -O bam 23 -O bam
24 -@ \$addthreads -m \$addmemory"M" 24 -@ \$addthreads -m \$addmemory"M"
65 <param name="addref_select" value="history" /> 65 <param name="addref_select" value="history" />
66 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> 66 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
67 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> 67 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
68 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> 68 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/>
69 </test> 69 </test>
70 <test>
71 <!-- Test direct use of bgzipped reference -->
72 <param name="addref_select" value="history" />
73 <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.bgzipped_fasta.gz" />
74 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
75 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/>
76 </test>
77 <test>
78 <!-- Test with simple gzipped reference, which requires decompression -->
79 <param name="addref_select" value="history" />
80 <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.fasta.gz" />
81 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
82 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/>
83 </test>
70 </tests> 84 </tests>
71 <help><![CDATA[ 85 <help><![CDATA[
72 **What it does** 86 **What it does**
73 87
74 Converts SAM dataset into its binary, BAM, representation using the ``samtools view`` and ``sort`` commands. 88 Converts SAM dataset into its binary, BAM, representation using the ``samtools view`` and ``sort`` commands.