Mercurial > repos > iuc > data_manager_homer_preparse
diff data_manager/homer_genome_preparse.xml @ 0:5d2e5fddec81 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"
author | iuc |
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date | Sun, 08 Aug 2021 10:57:48 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/homer_genome_preparse.xml Sun Aug 08 10:57:48 2021 +0000 @@ -0,0 +1,60 @@ +<tool id="homer_genome_preparse_data_manager" name="Homer genome preparse" tool_type="manage_data" version="@IDX_VERSION@" profile="20.05"> + <requirements> + <requirement type="package" version="@IDX_VERSION@">homer</requirement> + <requirement type="package" version="3.9">python</requirement> + </requirements> + <macros> + <token name="@IDX_VERSION@">4.11</token> + </macros> + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__/homer_genome_preparse.py' + '${out_file}' + --fasta_filename '${all_fasta_source.fields.path}' + --fasta_dbkey '${all_fasta_source.fields.dbkey}' + --fasta_description '${all_fasta_source.fields.name}' + ${mask} + --size '${size}' + --index_version '@IDX_VERSION@' + --data_table_name homer_preparse + ]]></command> + <inputs> + <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> + <options from_data_table="all_fasta"/> + </param> + <param name="sequence_name" type="text" value="" label="Name of sequence" /> + <param name="sequence_id" type="text" value="" label="ID for sequence" /> + <param name="mask" type="boolean" truevalue="--mask" falsevalue="" checked="False" label="mask repeats/lower case sequence" /> + <param name="size" type="integer" value="200" min="0" label="fragment size to use for motif finding" /> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> + <tests> + <test> + <param name="all_fasta_source" value="phiX174"/> + <output name="out_file" > + <assert_contents> + <has_text text="{"data_tables": {"homer_preparse": [{"dbkey": "phiX174", "mask": "False", "name": "phiX174 (200bp)", "path": "phiX174_200", "path_fasta":" /> + <has_text text="test-data/phiX174.fasta", "size": "200", "value": "phiX174_200", "version": "4.11"}]}}" /> + </assert_contents> + </output> + </test> + <test> + <param name="all_fasta_source" value="phiX174"/> + <param name="mask" value="True"/> + <param name="size" value="100"/> + <output name="out_file" > + <assert_contents> + <has_text text="{"data_tables": {"homer_preparse": [{"dbkey": "phiX174", "mask": "True", "name": "phiX174 masked (100bp)", "path": "phiX174r_100", "path_fasta":" /> + <has_text text="test-data/phiX174.fasta", "size": "100", "value": "phiX174r_100", "version": "4.11"}]}}" /> + </assert_contents> + </output> + </test> + </tests> + + <help> +.. class:: infomark + +**Notice:** If you leave name, description, or id blank, it will be generated automatically. + </help> +</tool>