Mercurial > repos > bgruening > instagraal
changeset 1:8d5b13b571fd draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/instagraal commit 3005cec91ca52f9d28aa2fe0bd4190555abafc35
author | bgruening |
---|---|
date | Sun, 13 Nov 2022 12:59:17 +0000 |
parents | 23d20e5e427d |
children | d1be552c6034 |
files | instagraal.xml tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample |
diffstat | 3 files changed, 47 insertions(+), 19 deletions(-) [+] |
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--- a/instagraal.xml Thu Nov 10 14:36:10 2022 +0000 +++ b/instagraal.xml Sun Nov 13 12:59:17 2022 +0000 @@ -28,11 +28,11 @@ ln -s '$fragments_list' hic_folder/fragments_list.txt && ln -s '$info_contigs' hic_folder/info_contigs.txt && -#if $reference_genome.source == 'history': +#if $ref_source.source == "history" #set $ref_genome = 'reference.fasta' - ln -s -f '${reference_genome.history_item}' $ref_genome && -#else: - #set $ref_genome = $reference_genome.index.fields.path + ln -s '${ref_source.ref_fasta}' $ref_genome && +#elif $ref_source.source == "builtin" + #set $ref_genome = '${ref_source.ref_fasta_builtin.fields.path}' #end if instagraal @@ -70,22 +70,19 @@ <param name="fragments_list" type="data" format="tabular" label="Fragments list"/> <param name="info_contigs" type="data" format="tabular" label="info_contigs"/> - <conditional name="reference_genome"> - <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options."> - <option value="indexed" selected="true">Use a built-in genome</option> - <option value="history">Use a genome from history</option> + <conditional name="ref_source"> + <param type="select" name="source" label="Reference genome source"> + <option value="history" selected="true">History</option> + <option value="builtin">Built-in</option> </param> - <when value="indexed"> - <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team."> - <options from_data_table="fasta_indexes"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No genomes are available for the selected input dataset" /> - </options> + <when value="history"> + <param type="data" format="fasta" name="ref_fasta" label="Reference genome" /> + </when> + <when value="builtin"> + <param type="select" name="ref_fasta_builtin" label="Reference genome"> + <options from_data_table="all_fasta" /> </param> </when> - <when value="history"> - <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" /> - </when> </conditional> <param argument="--level" type="integer" value="4" min="3" max="6" label="Level (resolution) of the contact map" @@ -116,9 +113,9 @@ <param name="abs_fragments_contacts_weighted" value="abs_fragments_contacts_weighted.tabular" /> <param name="fragments_list" value="fragments_list.tabular" /> <param name="info_contigs" value="info_contigs.tabular" /> - <conditional name="reference_genome"> + <conditional name="ref_source"> <param name="source" value="history"/> - <param name="history_item" value="fake.fasta" /> + <param name="ref_fasta" value="fake.fasta" /> </conditional> <assert_command> <has_text text="NNNNNNNNNN"/> <!-- 10 long, the default -->
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Sun Nov 13 12:59:17 2022 +0000 @@ -0,0 +1,18 @@ +#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_table_conf.xml.sample Sun Nov 13 12:59:17 2022 +0000 @@ -0,0 +1,13 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> + <!-- Locations of indexes in the hisat mapper format --> + <table name="hisat2_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/hisat2_indexes.loc" /> + </table> +</tables>