Mercurial > repos > geco-team > gmql_upload
diff gmql_rest_datasets_upload.xml @ 0:078d77023c34 draft default tip
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
| author | geco-team |
|---|---|
| date | Tue, 26 Jun 2018 08:59:19 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gmql_rest_datasets_upload.xml Tue Jun 26 08:59:19 2018 -0400 @@ -0,0 +1,266 @@ +<tool id="gmql_upload" name="GMLQ Upload Dataset" version="0.1.1"> + <macros> + <import>gmql_rest_macros.xml</import> + </macros> + <command><![CDATA[ + python $__tool_directory__/gmql_rest_datasets.py $output + -user=$authToken + -dataset=$name + #if $upload.source == 'remote' + -cmd=upload_url + #if $upload.schema.schema_type == "custom" : + -schema=$upload.schema.schema_url + #else : + -schema=$upload.schema.schema_type + #end if + -samples=$upload.samples_urls + #else: + -cmd=upload + #if $upload.schema_local.schema_type == "custom" : + -schema=$upload.schema_local.schema + #else : + -schema=$upload.schema_local.schema_type + #end if + -samples=$samples + #end if + -add_output=$updated_list + ]]></command> + <configfiles> + <configfile name="samples" >#if $upload.source == 'local' : + #if $upload.stype.st_flag == 'one' : + #echo '%s\t%s\n'%($upload.stype.samples.name,$upload.stype.samples) + #else : + #for $i in $upload.stype.samples : + #echo '%s\t%s\n'%($i.name,$i) + #end for + #end if + #end if + <!-- #if $upload.samples.is_collection : + #for $i in $upload.samples + #for $file in $i + #echo '%s\t%s\n'%($file.element_identifier,$file) + #end for + #else : + #echo '%s\t%s\n'%($i.name,$i) + #end if + #end for + #else : + #echo '%s\t%s\n'%($upload.samples.name,$upload.samples) + #end if + #end if --> + </configfile> + </configfiles> + <code file="dynamic_utils.py"> + <hook validate_input="validate_upload" /> + </code> + <inputs> + <param format="gmql_user" name="authToken" type="data" label="Select user" /> + <param name="name" type="text" label="Name of the new dataset" > + <validator type="regex" message="Only alphanumeric characters and underscore are allowed">[\w]+$</validator> + </param> + <conditional name="upload"> + <param name="source" type="select" label="Upload from local or another server" display="radio" multiple="false"> + <option value="local">Local</option> + <option value="remote">Provide Urls</option> + </param> + <when value="remote"> + <conditional name="schema"> + <param name="schema_type" type="select" label="File type" > + <option value="bed">bed</option> + <option value="bedGraph">bedGraph</option> + <option value="NarrowPeak">NarrowPeak</option> + <option value="BroadPeak">BroadPeak</option> + <option value="vcf">vcf</option> + <option value="custom">Custom</option> + </param> + <when value="custom"> + <param name="schema_url" type="text" format="text" size="80" label="Schema URL"> + <validator type="regex" message="Does not look as a valid url">[\w:/\.\?@#+-=&]+$</validator> + <sanitizer> + <valid initial="default"> + <remove value="&"/> + </valid> + <mapping initial="default"> + <add source="&" target="__amp__" /> + </mapping> + </sanitizer> + </param> + </when> + </conditional> + <param name="samples_urls" type="text" format="text" area="True" size="10x80" label="Samples URLs"> + <validator type="regex" message="Please one url per line">[\w:/\.\?@#+-=%&]+(\n[\w:/\.\?@#+-=%&]+)*$</validator> + <sanitizer> + <valid initial="default"> + <remove value="&"/> + </valid> + <mapping initial="default"> + <add source="X" target="__cn__" /> + <add source="&" target="__amp__" /> + </mapping> + </sanitizer> + </param> + </when> + <when value="local"> + <conditional name="schema_local"> + <param name="schema_type" type="select" label="File type" > + <option value="bed">bed</option> + <option value="bedGraph">bedGraph</option> + <option value="NarrowPeak">NarrowPeak</option> + <option value="BroadPeak">BroadPeak</option> + <option value="vcf">vcf</option> + <option value="custom">Custom</option> + </param> + <when value="custom"> + <param name="schema" type="data" format="xml" label="Schema XML Definition" /> + </when> + </conditional> + <conditional name="stype"> + <param name="st_flag" type="select" display="radio" label="Single Sample or Collection?"> + <option value="one">Single Sample</option> + <option value="more">Collection</option> + </param> + <when value="one"> + <param name="samples" type="data" label="Data: " /> + </when> + <when value="more"> + <param name="samples" type="data_collection" collection_type="list" label="Data: "/> + </when> + </conditional> + </when> + </conditional> + </inputs> + <outputs> + <data format="tabular" name="output" label="${name} updated samples" > + <actions> + <action name="column_names" type="metadata" default="id,sample,ext" /> + </actions> + </data> + <data format="gmql_repository" name="updated_list" label="${authToken.name.split()[0].rstrip('')} GMQL Datasets"> + <actions> + <action name="column_names" type="metadata" default="dataset,owner" /> + </actions> + </data> + </outputs> + <tests> + <test> + <param name="authToken" value="guest.gmql_user" /> + <param name="name" value="test1" /> + <conditional name="upload"> + <param name="source" value="remote" /> + <conditional name="schema"> + <param name="schema_type" value="custom" /> + <param name="schema_url" value="http://www.bioinformatics.deib.polimi.it/canakoglu/guest_data/HG19_ANN.schema" /> + </conditional> + <param name="samples_urls" value="http://www.bioinformatics.deib.polimi.it/canakoglu/guest_data/VistaEnhancers_hg19.bed" /> + </conditional> + <output name="updated_list" ftype="gmql_repository"> + <assert_contents> + <has_n_columns n="2" /> + <has_line_matching expression="test1\t.+" /> + </assert_contents> + </output> + <output name="output" ftype="gmql_repository"> + <metadata name="name" value="test1 updated samples" /> + <assert_contents> + <has_n_columns n="3" /> + <has_line_matching expression=".+\tVistaEnhancers_hg19\tbed.+" /> + </assert_contents> + </output> + </test> + <test> + <param name="authToken" value="guest.gmql_user" /> + <param name="name" value="test2" /> + <conditional name="upload"> + <param name="source" value="local" /> + <conditional name="schema_local"> + <param name="schema_type" value="bed" /> + </conditional> + <conditional name="stype"> + <param name="stflag" value="one" /> + <param name="samples" value="sample2.bed" /> + </conditional> + </conditional> + <output name="updated_list" ftype="gmql_repository"> + <assert_contents> + <has_n_columns n="2" /> + <has_line_matching expression="test2\t.+" /> + </assert_contents> + </output> + <output name="output" ftype="gmql_repository"> + <metadata name="name" value="test2 updated samples" /> + <assert_contents> + <has_n_columns n="3" /> + <has_text text="sample2" /> + </assert_contents> + </output> + </test> + <test> + <param name="authToken" value="guest.gmql_user" /> + <param name="name" value="test3" /> + <conditional name="upload"> + <param name="source" value="local" /> + <conditional name="schema_local"> + <param name="schema_type" value="bed" /> + </conditional> + <conditional name="stype"> + <param name="stflag" value="more" /> + <param name="samples"> + <collection type="list"> + <element name="sample1" value="sample1.bed" /> + <element name="sample2" value="sample2.bed" /> + </collection> + </param> + </conditional> + </conditional> + <output name="updated_list" ftype="gmql_repository"> + <assert_contents> + <has_n_columns n="2" /> + <has_line_matching expression="test3\t.+" /> + </assert_contents> + </output> + <output name="output" ftype="gmql_repository"> + <metadata name="name" value="test3 updated samples" /> + <assert_contents> + <has_n_columns n="3" /> + <has_text text="sample1" /> + <has_text text="sample2" /> + </assert_contents> + </output> + + </test> + </tests> + <help> +It allows uploading a new dataset on the user’s private space of the GMQL Repository. + +---- + +**What it does** + +- **Upload local data**: data to upload are in the current galaxy history +- **Upload remote data**: data is on a remote location, URLs must be provided + +The user must provide a name for the new dataset, the locations of the samples and their reference schema. Schema can +be a common type or custom. In this second case, schema xml or its location must be provided. + +.. class:: warningmark + +A gmql_user authentication token is required for every action. + +---- + +.. class:: infomark + +**File formats** + +Formats accepted for data are: + +- bed +- bedGraph +- NarrowPeak +- BroadPeak +- vcf + + + </help> + <expand macro="citations" /> +</tool>