Mercurial > repos > immuneml > immuneml_tools

changeset 16:cd57c1c66f8b draft

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"planemo upload commit 60f280176ecdc2883fc7e85deb9aaa151f7c2088"
author immuneml
date Wed, 05 Jan 2022 09:53:02 +0000
parents e33b3d370124
children b63bd4447c24
files immuneml_simulate_events.xml immuneml_train_ml_model.xml immuneml_train_recept.xml immuneml_train_repert.xml immuneml_yaml.xml
diffstat 5 files changed, 5 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/immuneml_simulate_events.xml	Tue Jan 04 12:57:42 2022 +0000
+++ b/immuneml_simulate_events.xml	Wed Jan 05 09:53:02 2022 +0000
@@ -21,7 +21,7 @@
       ]]>
   </command>
   <inputs>
-      <param name="iml_input" type="data" format="immuneml_receptors" label="Dataset input" optional="true" help="This field accepts datasets ithe ImmuneML format, as created by the Create Dataset tool."/>
+      <param name="iml_input" type="data" format="immuneml_receptors" label="immuneML dataset" optional="true" help="This field accepts datasets in the ImmuneML format, as created by the Create Dataset tool."/>
       <param name="yaml_input" type="data" format="txt" label="YAML specification" multiple="false"/>
   </inputs>
     <outputs>
--- a/immuneml_train_ml_model.xml	Tue Jan 04 12:57:42 2022 +0000
+++ b/immuneml_train_ml_model.xml	Wed Jan 05 09:53:02 2022 +0000
@@ -28,7 +28,7 @@
       ]]>
   </command>
   <inputs>
-      <param name="iml_input" type="data" format="immuneml_receptors" label="Dataset input" optional="true" help="This field accepts an ImmuneML dataset, as created by the Create Dataset tool."/>
+      <param name="iml_input" type="data" format="immuneml_receptors" label="immuneML dataset" optional="true" help="This field accepts an ImmuneML dataset, as created by the Create Dataset tool."/>
       <param name="yaml_input" type="data" format="txt" label="YAML specification" multiple="false"/>
       <param name="data_input" type="data" multiple="true" label="Additional files" optional="true" help="This field should include individual repertoire files, metadata files, receptor data and others."/>
   </inputs>
--- a/immuneml_train_recept.xml	Tue Jan 04 12:57:42 2022 +0000
+++ b/immuneml_train_recept.xml	Wed Jan 05 09:53:02 2022 +0000
@@ -50,7 +50,7 @@
       ]]>
 </command>
     <inputs>
-        <param name="iml_input" type="data" format="immuneml_receptors" label="Input dataset (immune receptors)" help="This field accepts receptor datasets in the ImmuneML dataset format, as created by the Create Dataset tool."/>
+        <param name="iml_input" type="data" format="immuneml_receptors" label="immuneML dataset (immune receptors)" help="This field accepts receptor datasets in the ImmuneML dataset format, as created by the Create Dataset tool."/>
         <param type="text" name="labels" optional="false" label="Which property (“label”) of the receptors would you like to predict?" help="A receptor property to predict could for example be the epitope it binds to. Such properties must be present as receptor sequence metadata. For example, when using data in VDJdb format, the default fields are named ‘epitope’, ‘epitope_gene’ and ‘epitope_species’. One of these labels must be chosen here."/>
 
         <conditional name="gap_cond">
--- a/immuneml_train_repert.xml	Tue Jan 04 12:57:42 2022 +0000
+++ b/immuneml_train_repert.xml	Wed Jan 05 09:53:02 2022 +0000
@@ -57,7 +57,7 @@
       ]]>
 </command>
     <inputs>
-        <param name="iml_input" type="data" format="immuneml_receptors"  label="Input dataset (immune repertoires)" help="Here you can select an ImmuneML dataset containing a repertoire dataset, as produced by the ‘Create dataset’ tool. Please make sure your dataset contains enough repertoires, we recommend using at least 50. The minimum number of repertoires needed to run this tool successfully is 14 (for example: 7 diseased and 7 healthy). More repertoires are needed if your dataset is imbalanced (many more diseased or many more healthy), or if you decrease the percentage of data that is used for training. "/>
+        <param name="iml_input" type="data" format="immuneml_receptors"  label="immuneML dataset (immune repertoires)" help="Here you can select an ImmuneML dataset containing a repertoire dataset, as produced by the ‘Create dataset’ tool. Please make sure your dataset contains enough repertoires, we recommend using at least 50. The minimum number of repertoires needed to run this tool successfully is 14 (for example: 7 diseased and 7 healthy). More repertoires are needed if your dataset is imbalanced (many more diseased or many more healthy), or if you decrease the percentage of data that is used for training. "/>
         <param type="text" name="labels" optional="false" label="Which property (“label”) of the repertoires would you like to predict?" help="Repertoire property to predict could for example be a disease status. This property must be present as a label in the repertoire metadata."/>
 
         <conditional name="sequence_cond">
--- a/immuneml_yaml.xml	Tue Jan 04 12:57:42 2022 +0000
+++ b/immuneml_yaml.xml	Wed Jan 05 09:53:02 2022 +0000
@@ -28,7 +28,7 @@
       ]]>
   </command>
   <inputs>
-      <param name="iml_input" type="data"  format="immuneml_receptors" label="ImmuneML dataset" optional="true" help="This field accepts ImmuneML datasets, as created by the Create Dataset tool."/>
+      <param name="iml_input" type="data"  format="immuneml_receptors" label="immuneML dataset" optional="true" help="This field accepts ImmuneML datasets, as created by the Create Dataset tool."/>
       <param name="yaml_input" type="data" format="txt" label="YAML specification" multiple="false"/>
       <param name="data_input" type="data" multiple="true" label="Additional files" optional="true" help="This field should include individual repertoire files, metadata files, receptor data and others."/>
   </inputs>