Mercurial > repos > iuc > sra_tools
comparison sam_dump.xml @ 18:7068f48d0ef9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
author | iuc |
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date | Mon, 08 Jun 2020 05:49:21 -0400 |
parents | aad3885b3216 |
children | 248f85ff0733 |
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17:c441583adae5 | 18:7068f48d0ef9 |
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1 <tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy1" profile="18.01"> | 1 <tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy0" profile="18.01"> |
2 <description>format from NCBI SRA</description> | 2 <description>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 <requirement type="package" version="1.10">samtools</requirement> | 7 <requirement type="package" version="1.10">samtools</requirement> |
8 </expand> | 8 </expand> |
9 <version_command>sam-dump --version</version_command> | 9 <version_command>sam-dump --version</version_command> |
10 <command detect_errors="exit_code"> | 10 <command detect_errors="exit_code"> |
11 <![CDATA[ | 11 <![CDATA[ |
12 @COPY_CONFIGFILE@ | |
12 @SET_ACCESSIONS@ | 13 @SET_ACCESSIONS@ |
13 | 14 |
14 ## Need to set the home directory to the current working directory, | |
15 ## else the tool tries to write to home/.ncbi and fails when used | |
16 ## with a cluster manager. | |
17 @CONFIGURE_TIMEOUT@ | |
18 vdb-config -s "/repository/user/main/public/root=\$PWD" && | |
19 ## Do not use prefetch if region is specified, to avoid downloading | 15 ## Do not use prefetch if region is specified, to avoid downloading |
20 ## the complete sra file. | 16 ## the complete sra file. |
21 | 17 |
22 #if $input.input_select == "file": | 18 #if $input.input_select == "file": |
23 sam-dump --log-level fatal '${input.file.name}' | 19 sam-dump --log-level fatal '${input.file.name}' |
24 #else: | 20 #else: |
25 #if ( str( $adv.region ) == "" ): | 21 #if ( str( $adv.region ) == "" ): |
26 prefetch -X 200000000 "\$acc" && | 22 prefetch -X 200000000 "\$acc" && |
27 ## Duplicate vdb-config, in case settings changed between prefetch and | |
28 ## dump command. | |
29 vdb-config -s "/repository/user/main/public/root=\$PWD" && | |
30 #end if | 23 #end if |
31 sam-dump --log-level fatal --disable-multithreading | 24 sam-dump --log-level fatal --disable-multithreading |
32 #end if | 25 #end if |
33 | 26 |
34 #if str( $adv.region ) != "": | 27 #if str( $adv.region ) != "": |
77 ) ; done | 70 ) ; done |
78 #end if | 71 #end if |
79 | 72 |
80 ]]> | 73 ]]> |
81 </command> | 74 </command> |
75 <expand macro="configfile_hack"/> | |
82 <inputs> | 76 <inputs> |
83 <expand macro="input_conditional"/> | 77 <expand macro="input_conditional"/> |
84 <param name="outputformat" type="select" display="radio" label="select output format" help="In vast majority of cases you want to download data in bam format. It is more compact and is accepted by all downstream tools."> | 78 <param name="outputformat" type="select" display="radio" label="select output format" help="In vast majority of cases you want to download data in bam format. It is more compact and is accepted by all downstream tools."> |
85 <option value="bam">bam</option> | 79 <option value="bam">bam</option> |
86 <option value="sam">sam</option> | 80 <option value="sam">sam</option> |
171 @ACCESSION_LIST_HOWTO@ | 165 @ACCESSION_LIST_HOWTO@ |
172 | 166 |
173 ----- | 167 ----- |
174 | 168 |
175 .. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf | 169 .. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf |
176 .. _sam-dump: http://ncbi.github.io/sra-tools/sam-dump.html | 170 .. _sam-dump: https://ncbi.github.io/sra-tools/sam-dump.html |
177 .. _collection: https://galaxyproject.org/tutorials/collections/ | 171 .. _collection: https://galaxyproject.org/tutorials/collections/ |
178 .. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies | 172 .. _link: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies |
179 | 173 |
180 @SRATOOLS_ATTRRIBUTION@ | 174 @SRATOOLS_ATTRRIBUTION@ |
181 ]]></help> | 175 ]]></help> |
182 <expand macro="citation"/> | 176 <expand macro="citation"/> |
183 </tool> | 177 </tool> |