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comparison samples_macros.xml @ 4:26ccb678abc8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
author iuc
date Tue, 19 Oct 2021 15:57:14 +0000
parents 9e2df763086c
children 6f6537780379
comparison
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3:59bb6d34fca6 4:26ccb678abc8
10 <param name="run_input_format" type="select" label="Select runs input format"> 10 <param name="run_input_format" type="select" label="Select runs input format">
11 <option value="multiple_selection_list" selected="True">Select individual datasets or datasets collection</option> 11 <option value="multiple_selection_list" selected="True">Select individual datasets or datasets collection</option>
12 <option value="paired_list" selected="False">Input from a paired collection</option> 12 <option value="paired_list" selected="False">Input from a paired collection</option>
13 </param> 13 </param>
14 <when value="multiple_selection_list"> 14 <when value="multiple_selection_list">
15 <param name="data" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="Select individual datasets or a dataset collection" help="Names should match the compressed run's files names defined in the metadata"/> 15 <param name="add_extension" type="boolean" checked="False" label="Add .fastq.(gz,.bz2) extension to the Galaxy dataset names to match the ones described in the input tables?"/>
16 <param name="data" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="Select individual datasets or a dataset collection" help="Names should match the compressed run's files names defined in the metadata"/>
16 </when> 17 </when>
17 <when value="paired_list"> 18 <when value="paired_list">
18 <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" label="List of paired-end runs files" help="Names should match the compressed run's files names defined in the metadata" /> 19 <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" label="List of paired-end runs files" help="Names should match the compressed run's files names defined in the metadata" />
19 </when> 20 </when>
20 </conditional> 21 </conditional>
21 </xml> 22 </xml>
22 <xml name="table_inputs_macro"> 23 <xml name="table_inputs_macro">
23 <conditional name="input_format_conditional"> 24 <conditional name="input_format_conditional">
38 <param name="samples_users_table" type="data" format="tabular" multiple="false" label="Samples table" help="Samples metadata file"/> 39 <param name="samples_users_table" type="data" format="tabular" multiple="false" label="Samples table" help="Samples metadata file"/>
39 <param name="experiments_users_table" type="data" format="tabular" multiple="false" label="Experiments table" help="Experiments metadata file"/> 40 <param name="experiments_users_table" type="data" format="tabular" multiple="false" label="Experiments table" help="Experiments metadata file"/>
40 <param name="runs_users_table" type="data" format="tabular" multiple="false" label="Runs table" help="Runs metadata file"/> 41 <param name="runs_users_table" type="data" format="tabular" multiple="false" label="Runs table" help="Runs metadata file"/>
41 </when> 42 </when>
42 <when value="build_tables"> 43 <when value="build_tables">
44 <param name="add_extension" type="boolean" checked="false" label="Add .fastq.(gz.bz2) extension to the Galaxy dataset names to match the ones described in the input tables?"/>
43 <conditional name="conditional_viral_metadata"> 45 <conditional name="conditional_viral_metadata">
44 <param name="viral_sample" type="boolean" truevalue="true" falsevalue="false" label="Does your submission contains viral samples?" /> 46 <param name="viral_sample" type="boolean" truevalue="true" falsevalue="false" label="Does your submission contains viral samples?" />
45 <when value="true"> 47 <when value="true">
46 <expand macro="viral_samples" /> 48 <expand macro="viral_samples" />
47 </when> 49 </when>
136 <options from_data_table="instrument_model"> 138 <options from_data_table="instrument_model">
137 <column name="value" index="0"/> 139 <column name="value" index="0"/>
138 </options> 140 </options>
139 </param> 141 </param>
140 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" > 142 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
141 <param name="run_base_name" type="text" optional="False" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/> 143 <param name="run_base_name" type="text" optional="False" value="" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/>
142 <param name="upload_files" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/> 144 <param name="upload_files" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/>
143 </repeat> 145 </repeat>
144 </repeat> 146 </repeat>
145 </repeat> 147 </repeat>
146 </repeat> 148 </repeat>
147 </xml> 149 </xml>
201 <options from_data_table="instrument_model"> 203 <options from_data_table="instrument_model">
202 <column name="value" index="0"/> 204 <column name="value" index="0"/>
203 </options> 205 </options>
204 </param> 206 </param>
205 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" > 207 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
206 <param name="run_base_name" type="text" optional="False" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/> 208 <param name="run_base_name" type="text" optional="False" value="" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/>
207 <param name="upload_files" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/> 209 <param name="upload_files" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/>
208 </repeat> 210 </repeat>
209 </repeat> 211 </repeat>
210 </repeat> 212 </repeat>
211 </repeat> 213 </repeat>
212 </xml> 214 </xml>