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comparison sam_dump.xml @ 2:6aa2efbe5920 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
author iuc
date Fri, 16 Sep 2016 17:23:44 -0400
parents 069a879beef7
children 62367c99119d
comparison
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1:069a879beef7 2:6aa2efbe5920
1 <tool id="sam_dump" name="Extract reads" version="1.3.0"> 1 <tool id="sam_dump" name="Extract reads" version="2.6.2">
2 <description>in SAM or BAM format from NCBI SRA.</description> 2 <description>in SAM or BAM format from NCBI SRA.</description>
3 <macros> 3 <macros>
4 <import>sra_macros.xml</import> 4 <import>sra_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
19 #end if 19 #end if
20 20
21 21
22 22
23 ## Need to set the home directory to the current working directory, 23 ## Need to set the home directory to the current working directory,
24 ## else the tool tries to write to home/.ncbi and fails when used 24 ## else the tool tries to write to home/.ncbi and fails when used
25 ## with a cluster manager. 25 ## with a cluster manager.
26 export HOME=\$PWD && 26 export HOME=\$PWD &&
27 vdb-config --restore-defaults && 27 vdb-config --restore-defaults &&
28 vdb-config -s "/repository/user/main/public/root=\$PWD" && 28 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
29 ## Do not use prefetch if region is specified, to avoid downloading 29 ## Do not use prefetch if region is specified, to avoid downloading
30 ## the complete sra file. 30 ## the complete sra file.
65 #elif $input.input_select == "accession_number": 65 #elif $input.input_select == "accession_number":
66 "\$acc" 66 "\$acc"
67 #elif $input.input_select=="file_list": 67 #elif $input.input_select=="file_list":
68 "\$acc" 68 "\$acc"
69 #end if 69 #end if
70 70
71 #if str( $outputformat ) == "bam": 71 #if str( $outputformat ) == "bam":
72 | samtools view -Sb - 2> /dev/null 72 | samtools view -Sb - 2> /dev/null
73 #end if 73 #end if
74 #if $input.input_select == "file": 74 #if $input.input_select == "file":
75 > "$output_file" 75 > "$output_file"
115 <outputs> 115 <outputs>
116 <collection name="output_collection" type='list'> 116 <collection name="output_collection" type='list'>
117 <filter>input['input_select'] == "file_list"</filter> 117 <filter>input['input_select'] == "file_list"</filter>
118 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.bam" directory="." ext='bam'/> 118 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.bam" directory="." ext='bam'/>
119 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.sam" directory="." ext='sam'/> 119 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.sam" directory="." ext='sam'/>
120 </collection> 120 </collection>
121 <data name="output_accession" format="bam" label="${input.accession}.${outputformat}"> 121 <data name="output_accession" format="bam" label="${input.accession}.${outputformat}">
122 <filter>input['input_select'] == "accession_number"</filter> 122 <filter>input['input_select'] == "accession_number"</filter>
123 <change_format> 123 <change_format>
124 <when input="outputformat" value="sam" format="sam"/> 124 <when input="outputformat" value="sam" format="sam"/>
125 </change_format> 125 </change_format>