| Previous changeset 3:8bbe09a52904 (2022-10-27) Next changeset 5:f9db47f68e5e (2023-04-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit a7400d366495a3e2bd6e0cb120834a59327537ec |
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modified:
pyega3.xml test-data/filelist3.tabular test-data/filelist_EGAD00001003338.tabular |
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| diff -r 8bbe09a52904 -r 9564758e8638 pyega3.xml --- a/pyega3.xml Thu Oct 27 15:12:30 2022 +0000 +++ b/pyega3.xml Wed Dec 07 15:26:17 2022 +0000 |
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| @@ -1,7 +1,7 @@ <tool id="pyega3" name="EGA Download Client" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.01" > <macros> <token name="@TOOL_VERSION@">4.0.5</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">pyega3</requirement> @@ -49,15 +49,14 @@ #elif $action.action_type == "download_files" #import re #set file_ids=[x.split('\t')[int(str($action.id_column))-1] for x in open(str($id_table)).readlines()] - #set outfiles=[x.split('\t')[int(str($action.file_column))-1].replace('\n', '') for x in open(str($id_table)).readlines()] mkdir downloads - #for f, o in zip($file_ids, $outfiles) + #for f in $file_ids #if not f.startswith("EGAF") && >&2 echo "Ignoring \"$f\": no EGA file ID" #continue #end if && - echo 'Downloading $f: $o' + echo 'Downloading $f' && pyega3 -c \${PYEGA_CONNECTIONS:-30} -cf '$credentials' fetch '$f' @@ -72,17 +71,8 @@ #end if #end if --output-dir downloads - #if re.match(".*vcf(_genomic_range_.*|).gz$", o) - #if $action.range.reference_name or ($action.range.start or $action.range.end) - && mv 'downloads/$f/'$o[:-3]'_genomic_range_'\$([ -z "$action.range.reference_name" ] && printf "None" || printf "$action.range.reference_name")'_'\$([ -z "$action.range.start" ] && printf "None" || printf "$action.range.reference_name")'_'\$([ -z "$action.range.reference_name" ] && printf "None" || printf "$action.range.end")'.gz' 'downloads/$f/'$o'.vcf_bgzip' - #else - && mv 'downloads/$f/$o' 'downloads/$f/'$o'.vcf_bgzip' - #end if - #end if - #if re.match(".*ped$", o) - && mv 'downloads/$f/$o' 'downloads/$f/'$o'.tabular' - #end if #end for + && for vcf in \$(ls downloads/**/*vcf.gz); do mv "\${vcf}" "\${vcf:0:-6}vcf_bgzip"; done ## renaming vcf.gz files to vcf_bgzip to recognize format && rm -f downloads/**/*.md5 ## checksum validation already performed by pyEGA, clean up downloads folder #end if @@ -128,7 +118,6 @@ <when value="download_files"> <param name="id_table" type="data" format="tabular" label="Table with IDs to download" help="A tabular file where one column contains the set of file IDs. This will output a collection. Please select files that are all the same format (e.g. all BAM or all VCF)."/> <param name="id_column" type="data_column" data_ref="id_table" label="Column containing the file IDs" help="File Identifiers starting with 'EGAF'. For example: EGAF00001753735" /> - <param name="file_column" type="data_column" data_ref="id_table" label="Column containing the file names" /> <section name="range" title="Request a specific Genomic range? (will be applied to ALL requested files)" expanded="false"> <param argument="--reference-name" type="text" optional="true" label="Reference Sequence Name" help="For example 'chr1', '1', or 'chrX'. If unspecified, all data is returned." /> <param argument="--start" type="integer" optional="true" min="0" label="Start Position" help="0-based, inclusive. Only used if a reference sequence name was specified"/> @@ -153,7 +142,7 @@ </data> <collection name="downloaded_file_collection" type="list" label="${tool.name} on ${on_string}: Downloaded datasets"> <filter> action['action_type'] == 'download_files' </filter> - <discover_datasets pattern="__designation_and_ext__" recurse="true" directory="downloads" /> + <discover_datasets pattern="__name_and_ext__" recurse="true" directory="downloads" /> </collection> </outputs> <tests> @@ -187,7 +176,13 @@ <param name="file_id" value="EGAF00001775036"/> <output name="downloaded_file" md5="3b89b96387db5199fef6ba613f70e27c"/> </test> - <!-- download a single file, with genomic range specified --> + <!-- download a single vcf.gz --> + <test expect_num_outputs="1"> + <param name="action_type" value="download_file"/> + <param name="file_id" value="EGAF00007243775"/> + <output name="downloaded_file" md5="51cfb69bf3b9416ff425381a58c18a2b" ftype="vcf_bgzip" /> + </test> + <!-- download a single bam, with genomic range specified --> <test expect_num_outputs="1"> <param name="action_type" value="download_file"/> <param name="file_id" value="EGAF00001753756"/> @@ -201,7 +196,6 @@ <param name="action_type" value="download_files"/> <param name="id_table" value="filelist.tabular"/> <param name="id_column" value="1"/> - <param name="file_column" value="5"/> <output_collection name="downloaded_file_collection" type="list" count="2"> <element name="ENCFF000VWO.bam" md5="b8ae14d5d1f717ab17d45e8fc36946a0" /> <element name="ENCFF284YOU.bam" md5="3b89b96387db5199fef6ba613f70e27c" /> @@ -215,7 +209,6 @@ <param name="action_type" value="download_files"/> <param name="id_table" value="filelist2.tabular"/> <param name="id_column" value="1"/> - <param name="file_column" value="5"/> <param name="reference_name" value="1"/> <param name="start" value="0"/> <param name="end" value="10000"/> @@ -232,10 +225,9 @@ <param name="action_type" value="download_files"/> <param name="id_table" value="filelist3.tabular"/> <param name="id_column" value="1"/> - <param name="file_column" value="5"/> <output_collection name="downloaded_file_collection" type="list" count="2"> - <element name="HG00408.novoBreak__256r__4.100100-10100100__7.200100-9000100.vcf.gz" md5="51cfb69bf3b9416ff425381a58c18a2b" /> - <element name="HG01890.HGSVC__145r__1.900100-10001000__18.2001000-90001000.vcf.gz" md5="ebad4425191a89d3e970c02190a87175" /> + <element name="HG00408.novoBreak__256r__4.100100-10100100__7.200100-9000100" md5="51cfb69bf3b9416ff425381a58c18a2b" ftype="vcf_bgzip" /> + <element name="HG01890.HGSVC__145r__1.900100-10001000__18.2001000-90001000" md5="ebad4425191a89d3e970c02190a87175" ftype="vcf_bgzip" /> </output_collection> </test> </tests> |
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| diff -r 8bbe09a52904 -r 9564758e8638 test-data/filelist3.tabular --- a/test-data/filelist3.tabular Thu Oct 27 15:12:30 2022 +0000 +++ b/test-data/filelist3.tabular Wed Dec 07 15:26:17 2022 +0000 |
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| @@ -1,3 +1,3 @@ File ID Status Bytes Check sum File name -EGAF00007243779 1 15340 ebad4425191a89d3e970c02190a87175 HG01890.HGSVC__145r__1.900100-10001000__18.2001000-90001000.vcf.gz -EGAF00007243775 1 23033 51cfb69bf3b9416ff425381a58c18a2b HG00408.novoBreak__256r__4.100100-10100100__7.200100-9000100.vcf.gz \ No newline at end of file +EGAF00007243779 1 15340 ebad4425191a89d3e970c02190a87175 HG01890.HGSVC__145r__1.900100-10001000__18.2001000-900010.vcf.gz +EGAF00007243775 1 23033 51cfb69bf3b9416ff425381a58c18a2b HG00408.novoBreak__256r__4.100100-10100100__7.200100-90001.vcf.gz \ No newline at end of file |
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| diff -r 8bbe09a52904 -r 9564758e8638 test-data/filelist_EGAD00001003338.tabular --- a/test-data/filelist_EGAD00001003338.tabular Thu Oct 27 15:12:30 2022 +0000 +++ b/test-data/filelist_EGAD00001003338.tabular Wed Dec 07 15:26:17 2022 +0000 |
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| @@ -59,3 +59,25 @@ EGAF00001770107 1 3551031027 dfef3f355230915418a78da460665d56 ENCFF284YOU.bam EGAF00001775034 1 5991400 b8ae14d5d1f717ab17d45e8fc36946a0 ENCFF000VWO.bam.bai EGAF00001775036 1 4804928 3b89b96387db5199fef6ba613f70e27c ENCFF284YOU.bam.bai +EGAF00007462299 1 15965067873 858d928a1a772cd0f1617ef72bae304e EE-2564.HG03520.alt_bwamem_GRCh38DH.20150718.ESN.low_coverage.bam +EGAF00007462300 1 7426229740 13a22b3eb197affaf69f5b25c2cad1b1 EE-2564.HG03520.alt_bwamem_GRCh38DH.20150718.ESN.low_coverage.cram +EGAF00007462301 1 69693619962 cca89d5791ebbac96fdb692a2894949f EE-2564.HGDP00862.alt_bwamem_GRCh38DH.20181023.Maya.bam +EGAF00007462302 1 34851312043 9ac1dddf1c2439ae4386658a32321624 EE-2564.HGDP00862.alt_bwamem_GRCh38DH.20181023.Maya.cram +EGAF00007462303 1 8200549586 6a5df1b7f6acc62b0320c2adeff6c000 EE-2564.NA18636.alt_bwamem_GRCh38DH.20150826.CHB.exome.bam +EGAF00007462304 1 4243466784 ed2b26633c18288410724224f3bdae41 EE-2564.NA18636.alt_bwamem_GRCh38DH.20150826.CHB.exome.cram +EGAF00007462305 1 68882266951 5746313dd819ba646b5f29830e0f2d50 EE-2564.SAMEA3302902.alt_bwamem_GRCh38DH.20200922.Karitiana.simons.bam +EGAF00007462306 1 37011545036 082d881341b21ed6e2b69e98da62a7db EE-2564.SAMEA3302902.alt_bwamem_GRCh38DH.20200922.Karitiana.simons.cram +EGAF00007462307 1 299199 ba85892ac1adb70b42e6635eacafe411 EE-2564.NA18636.alt_bwamem_GRCh38DH.20150826.CHB.exome.cram.crai +EGAF00007462308 1 1694742 8fc9df0e8a150acf0dd3b3df69a1a216 EE-2564.HGDP00862.alt_bwamem_GRCh38DH.20181023.Maya.cram.crai +EGAF00007462309 1 9515968 12ac8cc4ea178dfcb8736b4ebe45c531 EE-2564.SAMEA3302902.alt_bwamem_GRCh38DH.20200922.Karitiana.simons.bam.bai +EGAF00007462310 1 3706072 2cef86a5773cff9e337ad3ed57d545b7 EE-2564.NA18636.alt_bwamem_GRCh38DH.20150826.CHB.exome.bam.bai +EGAF00007462311 1 500587 e35f25f65c961aab2ab1cdc1e45ad824 EE-2564.HG03520.alt_bwamem_GRCh38DH.20150718.ESN.low_coverage.cram.crai +EGAF00007462312 1 9063136 e5c781c6d58dfd9a721ec4751d7acde2 EE-2564.HG03520.alt_bwamem_GRCh38DH.20150718.ESN.low_coverage.bam.bai +EGAF00007462313 1 2181685 ca047cdbacf5cd29720ca94098ac09fe EE-2564.SAMEA3302902.alt_bwamem_GRCh38DH.20200922.Karitiana.simons.cram.crai +EGAF00007462314 1 9548376 b2a36fc7043e807ad111c567120611bf EE-2564.HGDP00862.alt_bwamem_GRCh38DH.20181023.Maya.bam.bai +EGAF00007553556 1 14585114453 1377526fc26a58294635ba48edc35535 EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.genotypes.bcf +EGAF00007553557 1 16811693421 6b9e2acfc328ce13e6ce9ac745ac6561 EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.genotypes.vcf.gz +EGAF00007553558 1 2053513514 a6d323bb194eac03e7112c243aeef5d3 EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.genotypes_only_chr1and2.bcf +EGAF00007553559 1 2426228900 66bb08a031ff66c8c03ee9917be53fcf EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.genotypes_only_chr1and2.vcf.gz +EGAF00007553560 1 2691732 26d41f1a09671c834fd7b4eaac3f1a67 EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.genotypes.vcf.gz.tbi +EGAF00007553561 1 434009 357abb1556367d5c096cd54801a5e783 EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.genotypes_only_chr1and2.vcf.gz.tbi |