Mercurial > repos > rhpvorderman > data_manager_select_index_by_path
changeset 14:9ac9089b1914 draft
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 9ee0a33aa1c1e4b57b83244654f1f71a623b6247
| author | rhpvorderman |
|---|---|
| date | Tue, 03 Jul 2018 11:07:36 -0400 |
| parents | 0a1afc109ad9 |
| children | 0918549a5ff6 |
| files | README data_manager/data_manager_select_index_by_path.xml |
| diffstat | 2 files changed, 37 insertions(+), 26 deletions(-) [+] |
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--- a/README Tue Jul 03 10:29:48 2018 -0400 +++ b/README Tue Jul 03 11:07:36 2018 -0400 @@ -1,2 +1,11 @@ -This is a fork of the data_manager_all_fasta_by_path (https://github.com/Christian-B/galaxy_shedtools/tree/master/all_fasta_by_path) data manager by Cristian-B(https://github.com/Christian-B). -The all_fasta_by_path data manager was forked on 2017-09-07 from Christian-B's galaxy_shedtools (https://github.com/Christian-B/galaxy_shedtools) repository at commit d9f5343. +This is a fork of the data_manager_all_fasta_by_path data manager +by Cristian-B (https://github.com/Christian-B) +(https://github.com/Christian-B/galaxy_shedtools/tree/master/all_fasta_by_path). +The all_fasta_by_path data manager was forked on 2017-09-07 from +Christian-B's galaxy_shedtools repository at commit d9f5343. +(https://github.com/Christian-B/galaxy_shedtools). + +The tool has drastically changed since then, with a complete refactoring +of the python script and the addition of unit tests for all functionality +within the python script. A lot of indexes are now supported in addition to +just the all_fasta one. \ No newline at end of file
--- a/data_manager/data_manager_select_index_by_path.xml Tue Jul 03 10:29:48 2018 -0400 +++ b/data_manager/data_manager_select_index_by_path.xml Tue Jul 03 11:07:36 2018 -0400 @@ -12,8 +12,8 @@ --path "${path}" --data_table_name "${data_table}" --json_output_file "${json_output_file} - #if $data_table == "rnastar_index2" - --extra-columns {'with-gtf': '$data_table.with_gtf'} + #if $data_table_set.data_table == "rnastar_index2" + --extra-columns {'with-gtf': '$data_table_set.with_gtf'} #end if </command> <inputs> @@ -21,28 +21,30 @@ <param name="dbkey" type="text" value="" label="dbkey field for the entry. Defaults to value if left blank." /> <param name="name" type="text" value="" label="name field for the entry. Defaults to the file name from path if left blank." /> <param name="path" type="text" value="" label="path field for the entry" /> - <param name="data_table" type="select" value="" label="data table for the index"> - <option value='all_fasta'>all_fasta</option> - <option value='bowtie2_indexes'>bowtie2_indexes</option> - <option value='bowtie_indexes'>bowtie_indexes</option> - <option value='bowtie_indexes_color'>bowtie_indexes_color</option> - <option value='bwa_mem_indexes'>bwa_mem_indexes</option> - <option value='bwameth_indexes'>bwameth_indexes</option> - <option value='fasta_indexes'>fasta_indexes</option> - <option value='gatk_picard_indexes'>gatk_picard_indexes</option> - <option value='gene_transfer'>gene_transfer</option> - <option value='hisat2_indexes'>hisat2_indexes</option> - <option value='kallisto_indexes'>kallisto_indexes</option> - <option value='picard_indexes'>picard_indexes</option> - <option value='tophat2_indexes'>tophat2_indexes</option> - <option value="rnastar_index2">rnastar_index2</option> - <when value="rnastar_index2"> - <param name="with_gtf" type="select" value="" label="Index with embedded gtf?"> - <option value="0">No</option> - <option value="1">Yes</option> - </param> - </when> - </param> + <conditional name="data_table_set"> + <param name="data_table" type="select" value="" label="data table for the index"> + <option value='all_fasta'>all_fasta</option> + <option value='bowtie2_indexes'>bowtie2_indexes</option> + <option value='bowtie_indexes'>bowtie_indexes</option> + <option value='bowtie_indexes_color'>bowtie_indexes_color</option> + <option value='bwa_mem_indexes'>bwa_mem_indexes</option> + <option value='bwameth_indexes'>bwameth_indexes</option> + <option value='fasta_indexes'>fasta_indexes</option> + <option value='gatk_picard_indexes'>gatk_picard_indexes</option> + <option value='gene_transfer'>gene_transfer</option> + <option value='hisat2_indexes'>hisat2_indexes</option> + <option value='kallisto_indexes'>kallisto_indexes</option> + <option value='picard_indexes'>picard_indexes</option> + <option value='tophat2_indexes'>tophat2_indexes</option> + <option value="rnastar_index2">rnastar_index2</option> + <when value="rnastar_index2"> + <param name="with_gtf" type="select" value="" label="Index with embedded gtf?"> + <option value="0">No</option> + <option value="1">Yes</option> + </param> + </when> + </param> + </conditional> </inputs> <outputs> <data name="json_output_file" format="data_manager_json"/>