Mercurial > repos > ieguinoa > ena_webin_cli

comparison ena_consensus_submit.xml @ 1:f24eb2f2cb0c draft

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author ieguinoa
date Tue, 18 May 2021 21:00:09 +0000
parents e25357392813
children 1ecd8ce07db4
comparison
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0:e25357392813 1:f24eb2f2cb0c
38 mkdir fasta; 38 mkdir fasta;
39 39
40 echo -e "ASSEMBLY_TYPE\t$assembly_type" >> $manifest_base; 40 echo -e "ASSEMBLY_TYPE\t$assembly_type" >> $manifest_base;
41 echo -e "COVERAGE\t$coverage" >> $manifest_base; 41 echo -e "COVERAGE\t$coverage" >> $manifest_base;
42 echo -e "PROGRAM\t$assembly_program" >> $manifest_base; 42 echo -e "PROGRAM\t$assembly_program" >> $manifest_base;
43 echo -e "MINGAPLENGTH\t$min_gap_length" >> $manifest_base; 43 #if $min_gap_length:
44 echo -e "MINGAPLENGTH\t$min_gap_length" >> $manifest_base;
45 #end if
44 echo -e "MOLECULETYPE\t$molecule_type" >> $manifest_base; 46 echo -e "MOLECULETYPE\t$molecule_type" >> $manifest_base;
45 47
46 #if $metadata_file_or_form.metadata_format == "file": 48 #if $metadata_file_or_form.metadata_format == "file":
47 ## process the input tables, this creates an intermediate file with information 49 ## process the input tables, this creates an intermediate file with information
48 python3 '$__tool_directory__/process_input.py' $metadata_file_or_form.ena_receipt $genome_fasta './manifests' './fasta' $manifest_base; 50 python3 '$__tool_directory__/process_input.py' $metadata_file_or_form.ena_receipt $genome_fasta './manifests' './fasta' $manifest_base;
120 <param name="molecule_type" type="select" label="Molecule type"> 122 <param name="molecule_type" type="select" label="Molecule type">
121 <option value="genomic RNA" selected="True">genomic RNA</option> 123 <option value="genomic RNA" selected="True">genomic RNA</option>
122 <option value="viral cRNA">viral cRNA</option> 124 <option value="viral cRNA">viral cRNA</option>
123 <option value="genomic DNA">genomic DNA</option> 125 <option value="genomic DNA">genomic DNA</option>
124 </param> 126 </param>
125 <param name="min_gap_length" type="text" optional="True" label="Minimum gap length"/>
126 <param name="coverage" type="float" optional="False" value="10000" label="Coverage"/> 127 <param name="coverage" type="float" optional="False" value="10000" label="Coverage"/>
127 <conditional name="metadata_file_or_form"> 128 <conditional name="metadata_file_or_form">
128 <param name="metadata_format" type="select" label="Select the method to load study and sample metadata"> 129 <param name="metadata_format" type="select" label="Select the method to load study and sample metadata">
129 <option value="file" selected="True">I used Galaxy ENA upload tool for raw data submission, parse my submission receipt</option> 130 <option value="file" selected="True">I used Galaxy ENA upload tool for raw data submission, parse my submission receipt</option>
130 <option value="form">Fill in required metadata for linking</option> 131 <option value="form">Fill in required metadata for linking</option>
139 <param name="sequencing_platform" type="text" optional="False" label="Sequencing platform"/> 140 <param name="sequencing_platform" type="text" optional="False" label="Sequencing platform"/>
140 <param name="description" type="text" optional="True" value="" label="Description" help="Free text description of the genome assembly (optional)"/> 141 <param name="description" type="text" optional="True" value="" label="Description" help="Free text description of the genome assembly (optional)"/>
141 <param name="center_name" type="text" optional="False" label="Center name"/> 142 <param name="center_name" type="text" optional="False" label="Center name"/>
142 </when> 143 </when>
143 </conditional> 144 </conditional>
145 <param name="min_gap_length" type="text" optional="True" label="Minimum gap length (optional)"/>
144 </inputs> 146 </inputs>
145 <outputs> 147 <outputs>
146 <collection name="generated_manifests" type="list" label="Generated manifests"> 148 <collection name="generated_manifests" type="list" label="Generated manifests">
147 <!--<discover_datasets pattern="__name_and_ext__" directory="manifests" />--> 149 <!--<discover_datasets pattern="__name_and_ext__" directory="manifests" />-->
148 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.manifest\.txt$" ext="txt" directory="manifests" /> 150 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.manifest\.txt$" ext="txt" directory="manifests" />