Mercurial > repos > iuc > ena_upload

diff 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
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line diff
--- a/samples_macros.xml	Wed Aug 18 19:42:49 2021 +0000
+++ b/samples_macros.xml	Tue Oct 19 15:57:14 2021 +0000
@@ -12,10 +12,11 @@
                 <option value="paired_list" selected="False">Input from a paired collection</option>
             </param>
             <when value="multiple_selection_list">
-                <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"/>
+                <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?"/>
+                <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"/>
             </when>
             <when value="paired_list">
-                <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" />
+                <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" />
             </when>
         </conditional>
     </xml>
@@ -40,6 +41,7 @@
                 <param name="runs_users_table" type="data" format="tabular" multiple="false" label="Runs table" help="Runs metadata file"/>
             </when>
             <when value="build_tables">
+                <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?"/>
                 <conditional name="conditional_viral_metadata">
                     <param name="viral_sample" type="boolean" truevalue="true" falsevalue="false" label="Does your submission contains viral samples?" />
                     <when value="true">
@@ -138,8 +140,8 @@
                         </options>
                     </param>
                     <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
-                        <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"/>
-                        <param name="upload_files" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/>
+                        <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"/>
+                        <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"/>
                     </repeat>
                 </repeat>
             </repeat>
@@ -203,8 +205,8 @@
                     </options>
                 </param>
                 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
-                    <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"/>
-                    <param name="upload_files" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/>
+                    <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"/>
+                    <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"/>
                 </repeat>
             </repeat>
         </repeat>