| Previous changeset 1:c35d9902100e (2020-05-13) Next changeset 3:d648e40c6da9 (2020-06-07) |
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Commit message:
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d" |
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modified:
manta_macros.xml test-data/candidateSV.vcf.gz test-data/candidateSmallIndels.vcf.gz tool_data_table_conf.xml.sample |
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added:
test-data/cached_locally/fasta_indexes.loc test-data/fasta_indexes.loc tool-data/fasta_indexes.loc.sample |
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removed:
test-data/all_fasta.loc test-data/cached_locally/all_fasta.loc tool-data/all_fasta.loc.sample |
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| diff -r c35d9902100e -r 6a69e5d7c21f manta_macros.xml --- a/manta_macros.xml Wed May 13 15:42:33 2020 -0400 +++ b/manta_macros.xml Sun Jun 07 09:08:06 2020 -0400 |
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| @@ -1,7 +1,7 @@ <macros> <token name="@VERSION@">1.6</token> - <token name="@WRAPPER_VERSION@">@VERSION@+galaxy3</token> + <token name="@WRAPPER_VERSION@">@VERSION@+galaxy4</token> <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token> <token name="@set_reference_fasta_filename@"><![CDATA[ @@ -51,7 +51,7 @@ </param> <when value="cached"> <param name="index" type="select" label="Using reference genome" help="Select genome from the list"> - <options from_data_table="all_fasta"> + <options from_data_table="fasta_indexes"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" /> </options> |
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| diff -r c35d9902100e -r 6a69e5d7c21f test-data/all_fasta.loc --- a/test-data/all_fasta.loc Wed May 13 15:42:33 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,16 +0,0 @@ -#This file lists the locations and dbkeys of all the fasta files -#under the "genome" directory (a directory that contains a directory -#for each build). -This file has the format (white space characters are TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <file_path> -# -#So, it could look something like this: -# -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa -# -#Your .loc file should contain an entry for each individual -#fasta file. So there will be multiple fasta files for each build, -#such as with hg19 above. -hg19 hg19 Human hg19 ${__HERE__}/cached_locally/cached_region.fa |
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| diff -r c35d9902100e -r 6a69e5d7c21f test-data/cached_locally/all_fasta.loc --- a/test-data/cached_locally/all_fasta.loc Wed May 13 15:42:33 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -hg19 hg19 Human hg19 ${__HERE__}/cached_region.fa |
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| diff -r c35d9902100e -r 6a69e5d7c21f test-data/cached_locally/fasta_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/fasta_indexes.loc Sun Jun 07 09:08:06 2020 -0400 |
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| @@ -0,0 +1,1 @@ +hg19 hg19 Human hg19 ${__HERE__}/cached_region.fa |
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| diff -r c35d9902100e -r 6a69e5d7c21f test-data/candidateSV.vcf.gz |
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| Binary file test-data/candidateSV.vcf.gz has changed |
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| diff -r c35d9902100e -r 6a69e5d7c21f test-data/candidateSmallIndels.vcf.gz |
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| Binary file test-data/candidateSmallIndels.vcf.gz has changed |
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| diff -r c35d9902100e -r 6a69e5d7c21f test-data/fasta_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Sun Jun 07 09:08:06 2020 -0400 |
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| @@ -0,0 +1,31 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/sam_indexes/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /path/to/genome/hg18/sam_indexes/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /path/to/genome/sam_indexes/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/sam_indexes/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/sam_indexes/hg19full.fa + +hg19 hg19 Human hg19 ${__HERE__}/cached_locally/cached_region.fa |
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| diff -r c35d9902100e -r 6a69e5d7c21f tool-data/all_fasta.loc.sample --- a/tool-data/all_fasta.loc.sample Wed May 13 15:42:33 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,15 +0,0 @@ -#This file lists the locations and dbkeys of all the fasta files -#under the "genome" directory (a directory that contains a directory -#for each build). -This file has the format (white space characters are TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <file_path> -# -#So, it could look something like this: -# -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa -# -#Your .loc file should contain an entry for each individual -#fasta file. So there will be multiple fasta files for each build, -#such as with hg19 above. |
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| diff -r c35d9902100e -r 6a69e5d7c21f tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Sun Jun 07 09:08:06 2020 -0400 |
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| @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/sam_indexes/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /path/to/genome/hg18/sam_indexes/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /path/to/genome/sam_indexes/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/sam_indexes/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/sam_indexes/hg19full.fa \ No newline at end of file |
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| diff -r c35d9902100e -r 6a69e5d7c21f tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Wed May 13 15:42:33 2020 -0400 +++ b/tool_data_table_conf.xml.sample Sun Jun 07 09:08:06 2020 -0400 |
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| @@ -1,6 +1,6 @@ <tables> - <table name="all_fasta" comment_char="#"> + <table name="fasta_indexes" comment_char="#"> <columns>value, dbkey, name, path</columns> - <file path="${__HERE__}/test-data/all_fasta.loc" /> + <file path="${__HERE__}/test-data/fasta_indexes.loc" /> </table> </tables> |