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comparison sam_dump.xml @ 1:069a879beef7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 8550e0c7389533bebc75d7a93b89a3e59fe77bcd
author iuc
date Tue, 17 May 2016 13:55:57 -0400
parents 20da3b075bbf
children 6aa2efbe5920
comparison
equal deleted inserted replaced
0:20da3b075bbf 1:069a879beef7
1 <tool id="sam_dump" name="Extract reads" version="1.2.5"> 1 <tool id="sam_dump" name="Extract reads" version="1.3.0">
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"/>
7 <version_command>sam-dump --version</version_command> 7 <version_command>sam-dump --version</version_command>
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 #if $input.input_select=="file_list":
11 for acc in `cat $input.file_list` ;
12 do
13 #elif $input.input_select=="accession_number":
14 acc="$input.accession" &&
15 #end if
16
17 #if $input.input_select=="file_list" or $input.input_select=="accession_number":
18 [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
19 #end if
20
21
22
10 ## Need to set the home directory to the current working directory, 23 ## Need to set the home directory to the current working directory,
11 ## 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
12 ## with a cluster manager. 25 ## with a cluster manager.
13 export HOME=\$PWD && 26 export HOME=\$PWD &&
14 vdb-config --restore-defaults && 27 vdb-config --restore-defaults &&
16 ## Do not use prefetch if region is specified, to avoid downloading 29 ## Do not use prefetch if region is specified, to avoid downloading
17 ## the complete sra file. 30 ## the complete sra file.
18 #if ( str( $adv.region ) == "" ): 31 #if ( str( $adv.region ) == "" ):
19 ASCP_PATH=`command -v ascp` && 32 ASCP_PATH=`command -v ascp` &&
20 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true && 33 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
21 prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession" && 34 prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
22 ## Duplicate vdb-config, in case settings changed between prefetch and 35 ## Duplicate vdb-config, in case settings changed between prefetch and
23 ## dump command. 36 ## dump command.
24 vdb-config -s "/repository/user/main/public/root=\$PWD" && 37 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
25 #end if 38 #end if
26 sam-dump --log-level fatal --disable-multithreading 39 sam-dump --log-level fatal --disable-multithreading
48 --primary 61 --primary
49 #end if 62 #end if
50 #if $input.input_select == "file": 63 #if $input.input_select == "file":
51 "$input.file" 64 "$input.file"
52 #elif $input.input_select == "accession_number": 65 #elif $input.input_select == "accession_number":
53 "$input.accession" 66 "\$acc"
67 #elif $input.input_select=="file_list":
68 "\$acc"
54 #end if 69 #end if
70
55 #if str( $outputformat ) == "bam": 71 #if str( $outputformat ) == "bam":
56 | samtools view -Sb - 2> /dev/null 72 | samtools view -Sb - 2> /dev/null
57 #end if 73 #end if
58 #if $input.input_select == "file": 74 #if $input.input_select == "file":
59 > "$output_file" 75 > "$output_file"
60 #elif $input.input_select == "accession_number": 76 #elif $input.input_select == "accession_number":
61 > "$output_accession" 77 > "$output_accession" )
62 #end if 78 #end if
79
80 #if $input.input_select=="file_list":
81 #if str( $outputformat ) == "bam":
82 > "\$acc.bam"
83 #elif str( $outputformat ) == "sam":
84 > "\$acc.sam"
85 #end if
86 ) ; done
87 #end if
88
89
63 ]]> 90 ]]>
64 </command> 91 </command>
65 <inputs> 92 <inputs>
66 <expand macro="input_conditional"/> 93 <expand macro="input_conditional"/>
67 <param name="outputformat" type="select" label="select output format"> 94 <param name="outputformat" type="select" label="select output format">
84 </param> 111 </param>
85 <expand macro="minMapq"></expand> 112 <expand macro="minMapq"></expand>
86 </section> 113 </section>
87 </inputs> 114 </inputs>
88 <outputs> 115 <outputs>
116 <collection name="output_collection" type='list'>
117 <filter>input['input_select'] == "file_list"</filter>
118 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.bam" directory="." ext='bam'/>
119 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.sam" directory="." ext='sam'/>
120 </collection>
89 <data name="output_accession" format="bam" label="${input.accession}.${outputformat}"> 121 <data name="output_accession" format="bam" label="${input.accession}.${outputformat}">
90 <filter>input['input_select'] == "accession_number"</filter> 122 <filter>input['input_select'] == "accession_number"</filter>
91 <change_format> 123 <change_format>
92 <when input="outputformat" value="sam" format="sam"/> 124 <when input="outputformat" value="sam" format="sam"/>
93 </change_format> 125 </change_format>