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confirm academic usage
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@nilchia
nilchia committed Aug 6, 2024
1 parent 8829a39 commit 12156b4
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89 changes: 11 additions & 78 deletions tools/flexynesis/flexynesis.xml
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Expand Up @@ -54,87 +54,20 @@
$disable_marker_finding
]]></command>
<inputs>
<param name="train" type="data" format="csv" multiple="true" label="Train data" help="You need one clin.csv and at least one omics.csv"/>
<param name="test" type="data" format="csv" multiple="true" label="Test data" help="You need one clin.csv and at least one omics.csv"/>
<param argument="--data_types" type="text" optional="false" label="Data types" help="Which omics data matrices to work on; comma-separated (e.g., 'gex,cnv').">
<sanitizer invalid_char="">
<valid initial="string.printable"></valid>
</sanitizer>
</param>
<conditional name="training_type">
<param name="model" type="select" label="Type of Analysis" >
<option value="s_train">Supervised training</option>
<option value="us_train">Unsupervised Training</option>
<option value="cm_train">Cross-modality Training</option>
<conditional name="license" label="LICENSE">
<param name="license" type="select" label="Please confirm to proceed." help="Permission is only granted for ACADEMIC, RESEARCH, and EDUCATIONAL usage. For commercial use please contact copyright holders.">
<option value=""></option>
<option value="academic">I confirm to use this tool only for ACADEMIC, RESEARCH, or EDUCATIONAL purposes</option>
<option value="commercial">I use this tool for commercial purpose but I HAVE explicit permission</option>
</param>
<when value="s_train">
<conditional name="model_class" label="Model class">
<param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
<option value="DirectPred">DirectPred</option>
<option value="GNN">GNN</option>
<option value="MultiTripletNetwork">MultiTripletNetwork</option>
<option value="RandomForest">RandomForest</option>
<option value="SVM">SVM</option>
<option value="RandomSurvivalForest">RandomSurvivalForest</option>
</param>
<when value="DirectPred"></when>
<when value="GNN">
<param argument="--gnn_conv_type" type="select" label="GNN convolution type" help="Which graph convolution type to use.">
<option value="GC">GC</option>
<option value="GCN">GCN</option>
<option value="SAGE">SAGE</option>
</param>
<param argument="--string_organism" type="integer" value="9606" label="string organism" help="STRING DB organism id. Default is 9606 (Homo Sapiens)." />
<param argument="--string_node_name" type="select" label="String node name" help="">
<option value="gene_name">Gene name</option>
<option value="gene_id">Gene id</option>
</param>
</when>
<when value="MultiTripletNetwork"></when>
<when value="RandomForest"></when>
<when value="SVM"></when>
<when value="RandomSurvivalForest"></when>
</conditional>
<param argument="--target_variables" type="text" label="Target variables" help="Which variables in 'clin.csv' to use for predictions, comma-separated if multiple.">
<sanitizer invalid_char="">
<valid initial="string.printable"></valid>
</sanitizer>
</param>
<param argument="--surv_event_var" type="text" label="Survival event" help="Which column in 'clin.csv' to use as event/status indicator for survival modeling.">
<sanitizer invalid_char="">
<valid initial="string.printable"></valid>
</sanitizer>
</param>
<param argument="--surv_time_var" type="text" label="Survival time" help="Which column in 'clin.csv' to use as time/duration indicator for survival modeling.">
<sanitizer invalid_char="">
<valid initial="string.printable"></valid>
</sanitizer>
</param>
<expand macro="advanced"/>
<when value=""></when>
<when value="academic">
<expand macro="all_param"/>
</when>
<when value="us_train">
<param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
<option value="supervised_vae">supervised_vae</option>
</param>
<expand macro="advanced"/>
<when value="commercial">
<expand macro="all_param"/>
</when>
<when value="cm_train">
<param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
<option value="CrossModalPred">CrossModalPred</option>
</param>
<param argument="--input_layers" type="text" label="Input layers" help="Which data types to use as input/encoded layers, comma-separated if multiple.">
<sanitizer invalid_char="">
<valid initial="string.printable"></valid>
</sanitizer>
</param>
<param argument="--output_layers" type="text" label="Output layers" help="Which data types to use as output/decoded layers, comma-separated if multiple.">
<sanitizer invalid_char="">
<valid initial="string.printable"></valid>
</sanitizer>
</param>
<expand macro="advanced"/>
</when>
</conditional>
</conditional>
</inputs>
<outputs>
<collection name="results" type="list" label="${tool.name} on ${on_string}: flexynesis results">
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84 changes: 83 additions & 1 deletion tools/flexynesis/macros.xml
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Expand Up @@ -43,7 +43,89 @@
<param argument="--disable_marker_finding" type="boolean" truevalue="--disable_marker_finding" falsevalue="" checked="false" label="Disable marker finding" help="f set, marker discovery after model training is disabled." />
</section>
</xml>

<xml name="all_param">
<param name="train" type="data" format="csv" multiple="true" label="Train data" help="You need one clin.csv and at least one omics.csv"/>
<param name="test" type="data" format="csv" multiple="true" label="Test data" help="You need one clin.csv and at least one omics.csv"/>
<param argument="--data_types" type="text" optional="false" label="Data types" help="Which omics data matrices to work on; comma-separated (e.g., 'gex,cnv').">
<sanitizer invalid_char="">
<valid initial="string.printable"></valid>
</sanitizer>
</param>
<conditional name="training_type">
<param name="model" type="select" label="Type of Analysis" >
<option value="s_train">Supervised training</option>
<option value="us_train">Unsupervised Training</option>
<option value="cm_train">Cross-modality Training</option>
</param>
<when value="s_train">
<conditional name="model_class" label="Model class">
<param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
<option value="DirectPred">DirectPred</option>
<option value="GNN">GNN</option>
<option value="MultiTripletNetwork">MultiTripletNetwork</option>
<option value="RandomForest">RandomForest</option>
<option value="SVM">SVM</option>
<option value="RandomSurvivalForest">RandomSurvivalForest</option>
</param>
<when value="DirectPred"></when>
<when value="GNN">
<param argument="--gnn_conv_type" type="select" label="GNN convolution type" help="Which graph convolution type to use.">
<option value="GC">GC</option>
<option value="GCN">GCN</option>
<option value="SAGE">SAGE</option>
</param>
<param argument="--string_organism" type="integer" value="9606" label="string organism" help="STRING DB organism id. Default is 9606 (Homo Sapiens)." />
<param argument="--string_node_name" type="select" label="String node name" help="">
<option value="gene_name">Gene name</option>
<option value="gene_id">Gene id</option>
</param>
</when>
<when value="MultiTripletNetwork"></when>
<when value="RandomForest"></when>
<when value="SVM"></when>
<when value="RandomSurvivalForest"></when>
</conditional>
<param argument="--target_variables" type="text" label="Target variables" help="Which variables in 'clin.csv' to use for predictions, comma-separated if multiple.">
<sanitizer invalid_char="">
<valid initial="string.printable"></valid>
</sanitizer>
</param>
<param argument="--surv_event_var" type="text" label="Survival event" help="Which column in 'clin.csv' to use as event/status indicator for survival modeling.">
<sanitizer invalid_char="">
<valid initial="string.printable"></valid>
</sanitizer>
</param>
<param argument="--surv_time_var" type="text" label="Survival time" help="Which column in 'clin.csv' to use as time/duration indicator for survival modeling.">
<sanitizer invalid_char="">
<valid initial="string.printable"></valid>
</sanitizer>
</param>
<expand macro="advanced"/>
</when>
<when value="us_train">
<param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
<option value="supervised_vae">supervised_vae</option>
</param>
<expand macro="advanced"/>
</when>
<when value="cm_train">
<param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
<option value="CrossModalPred">CrossModalPred</option>
</param>
<param argument="--input_layers" type="text" label="Input layers" help="Which data types to use as input/encoded layers, comma-separated if multiple.">
<sanitizer invalid_char="">
<valid initial="string.printable"></valid>
</sanitizer>
</param>
<param argument="--output_layers" type="text" label="Output layers" help="Which data types to use as output/decoded layers, comma-separated if multiple.">
<sanitizer invalid_char="">
<valid initial="string.printable"></valid>
</sanitizer>
</param>
<expand macro="advanced"/>
</when>
</conditional>
</xml>
<xml name="citations">
<citations>
<citation type="doi">10.1101/2024.07.16.603606</citation>
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