Mercurial > repos > thondeboer > neat_genreads
changeset 10:7d10b55965c9 draft default tip
planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
| author | thondeboer |
|---|---|
| date | Wed, 16 May 2018 17:02:51 -0400 |
| parents | 441103f02a11 |
| children | |
| files | computeGC.xml genMutModel.xml neat_genreads.xml test-data/fasta_indexes.loc tool-data/all_fasta.loc.sample tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 8 files changed, 106 insertions(+), 25 deletions(-) [+] |
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--- a/computeGC.xml Wed May 16 02:05:26 2018 -0400 +++ b/computeGC.xml Wed May 16 17:02:51 2018 -0400 @@ -45,7 +45,7 @@ type="select" label="Select a built-in reference sequence" help="The reference sequence that will be used as the basis for the simulated reads"> - <options from_data_table="all_fasta" /> + <options from_data_table="fasta_indexes" /> </param> </when> <when value="history">
--- a/genMutModel.xml Wed May 16 02:05:26 2018 -0400 +++ b/genMutModel.xml Wed May 16 17:02:51 2018 -0400 @@ -50,7 +50,7 @@ type="select" label="Select a built-in reference sequence" help="The reference sequence that will be used as the basis for the simulated reads"> - <options from_data_table="all_fasta" /> + <options from_data_table="fasta_indexes" /> </param> </when> <when value="history"> @@ -180,5 +180,16 @@ <output name="trinuc_file" value="chrMT.fa.trinucCounts" compare="diff"/> </test> + <test> + <conditional name="in_type"> + <param name="input_type" value="built-in"/> + <param name="reference" value="hg19chrmt" format="fasta"> + <options from_data_table="fasta_indexes" /> + </param> + </conditional> + <param name="mutation_file" value="chrMT-PE-VCF-BAM.vcf"/> + <output name="genMutModel_modelfile" value="chrMT-PE-VCF-BAM-genMutModel.p" compare="diff"/> + </test> + </tests> </tool> \ No newline at end of file
--- a/neat_genreads.xml Wed May 16 02:05:26 2018 -0400 +++ b/neat_genreads.xml Wed May 16 17:02:51 2018 -0400 @@ -97,7 +97,7 @@ type="select" label="Select a built-in reference sequence" help="The reference sequence that will be used as the basis for the simulated reads"> - <options from_data_table="all_fasta" /> + <options from_data_table="fasta_indexes" /> </param> </when> <when value="history"> @@ -627,6 +627,28 @@ <assert_stdout has_text="Writing output VCF..."/> </test> - + <test> + <conditional name="in_type"> + <param name="input_type" value="built-in"/> + <param name="reference" value="hg19chrmt" format="fasta"> + <options from_data_table="fasta_indexes" /> + </param> + </conditional> + <conditional name="lib_type_cond"> + <param name="lib_type" value="single"/> + </conditional> + <section name="stats"> + <param name="seed" value="1"/> + </section> + <param name="read_length" value="101"/> + <section name="out_options"> + <param name="prefix" value="out"/> + <param name="golden_bam" value="false"/> + <param name="golden_vcf" value="false"/> + <param name="compress" value="false"/> + </section> + <output name="out_file1" file="chrMT_read1.fq" compare="diff"/> + </test> + </tests> </tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Wed May 16 17:02:51 2018 -0400 @@ -0,0 +1,30 @@ +#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 /depot/data2/galaxy/hg19/sam/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 /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa +hg19chrmt hg19 Human (Homo sapiens): hg19 chrMT ${__HERE__}/chrMT.fa \ No newline at end of file
--- a/tool-data/all_fasta.loc.sample Wed May 16 02:05:26 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +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). The script extract_fasta.py will generate the file -#all_fasta.loc. This file has the format (white space characters are -#TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <file_path> -# -#So, all_fasta.loc could look something like this: -# -#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa -#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 all_fasta.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. -#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Wed May 16 17:02:51 2018 -0400 @@ -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 /depot/data2/galaxy/hg19/sam/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 /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa \ No newline at end of file
--- a/tool_data_table_conf.xml.sample Wed May 16 02:05:26 2018 -0400 +++ b/tool_data_table_conf.xml.sample Wed May 16 17:02:51 2018 -0400 @@ -1,7 +1,7 @@ <tables> - <!-- Locations of all fasta files under genome directory --> - <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <!-- Locations of all sam indexes under genome directory --> + <table name="fasta_indexes" comment_char="#"> <columns>value, dbkey, name, path</columns> - <file path="tool-data/all_fasta.loc" /> + <file path="tool-data/fasta_indexes.loc" /> </table> </tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed May 16 17:02:51 2018 -0400 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all sam indexes under genome directory --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/fasta_indexes.loc" /> + </table> +</tables> \ No newline at end of file