Mercurial > repos > immuneml > immuneml_tools

changeset 3:ed3932e6d616 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
author immuneml
date Thu, 01 Jul 2021 16:51:28 +0000
parents 9bf78cb6b91d
children 697bb1a18bc7
files README.md README.rst immuneml_create_dataset.xml immuneml_simulate_dataset.xml immuneml_simulate_events.xml immuneml_train_ml_model.xml immuneml_train_recept.xml immuneml_train_repert.xml immuneml_yaml.xml
diffstat 9 files changed, 12 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/README.md	Thu Jul 01 14:43:41 2021 +0000
+++ b/README.md	Thu Jul 01 16:51:28 2021 +0000
@@ -5,7 +5,7 @@
 ## Installation:
 The tools can be installed from a Galaxy toolshed. You can also install them offline by editing Galaxy config files in the usual way.
 
-### New datatype `iml_dataset`
+### New datatype `immuneml_receptors`
 No matter how you install the tools, you will need to define a new datatype, which is done as follows:
 
 1. In your `galaxy.yml` look up the name of your `datatypes_config_file`. If the name is not yet defined, set
@@ -15,7 +15,7 @@
 2. Make `datatypes_conf.xml` by copying `datatypes_conf.xml.sample` unless a `datatypes_config_file` was already defined.
 3. Add the following line to your `datatypes_config_file`:
 ```
-<datatype extension="iml_dataset" type="galaxy.datatypes.text:Html" subclass="True"/>
+<datatype extension="immuneml_receptors" type="galaxy.datatypes.text:Html" subclass="True"/>
 ```
 The line has to be inside `<registration>` along with the other datatypes.
 
--- a/README.rst	Thu Jul 01 14:43:41 2021 +0000
+++ b/README.rst	Thu Jul 01 16:51:28 2021 +0000
@@ -1,6 +1,6 @@
 Installation
 ============
-You will need to define a new datatype, which is done as follows:
+You will need to define a new datatype ``immuneml_receptors``, which is done as follows:
 
 1. In your ``galaxy.yml`` look up the name of your ``datatypes_config_file``. If the name is not yet defined, set
 
@@ -9,7 +9,7 @@
 2. Make ``datatypes_conf.xml`` by copying ``datatypes_conf.xml.sample`` unless a ``datatypes_config_file`` was already defined.
 3. Add the following line to your ``datatypes_config_file``:
 
-``<datatype extension="iml_dataset" type="galaxy.datatypes.text:Html" subclass="True"/>``
+``<datatype extension="immuneml_receptors" type="galaxy.datatypes.text:Html" subclass="True"/>``
 The line has to be inside ``<registration>`` along with the other datatypes.
 
 The immuneML conda package
--- a/immuneml_create_dataset.xml	Thu Jul 01 14:43:41 2021 +0000
+++ b/immuneml_create_dataset.xml	Thu Jul 01 16:51:28 2021 +0000
@@ -137,7 +137,7 @@
   </inputs>
     <outputs>
         <data format="txt" name="specs" label="create_dataset.yaml"/>
-        <data format="iml_dataset" name="html_outfile" label="ImmuneML dataset"/>
+        <data format="immuneml_receptors" name="html_outfile" label="ImmuneML dataset"/>
     </outputs>
 
 
--- a/immuneml_simulate_dataset.xml	Thu Jul 01 14:43:41 2021 +0000
+++ b/immuneml_simulate_dataset.xml	Thu Jul 01 16:51:28 2021 +0000
@@ -19,7 +19,7 @@
   </inputs>
     <outputs>
         <data format="zip" name="archive" label="Archive: dataset simulation"/>
-        <data format="iml_dataset" name="html_outfile" label="ImmuneML dataset (simulated sequences)"/>
+        <data format="immuneml_receptors" name="html_outfile" label="ImmuneML dataset (simulated sequences)"/>
     </outputs>
 
 
--- a/immuneml_simulate_events.xml	Thu Jul 01 14:43:41 2021 +0000
+++ b/immuneml_simulate_events.xml	Thu Jul 01 16:51:28 2021 +0000
@@ -22,11 +22,11 @@
   </command>
   <inputs>
       <param name="yaml_input" type="data" format="txt" label="YAML specification" multiple="false"/>
-      <param name="iml_input" type="data" format="iml_dataset" label="Dataset input" optional="true" help="This field accepts datasets in iml_dataset format, as created by the Create Dataset tool."/>
+      <param name="iml_input" type="data" format="immuneml_receptors" label="Dataset input" optional="true" help="This field accepts datasets in iml_dataset format, as created by the Create Dataset tool."/>
   </inputs>
     <outputs>
         <data format="zip" name="archive" label="Archive: immune signal simulation"/>
-        <data format="iml_dataset" name="html_outfile" label="ImmuneML dataset (simulated immune signals)"/>
+        <data format="immuneml_receptors" name="html_outfile" label="ImmuneML dataset (simulated immune signals)"/>
     </outputs>
 
 
--- a/immuneml_train_ml_model.xml	Thu Jul 01 14:43:41 2021 +0000
+++ b/immuneml_train_ml_model.xml	Thu Jul 01 16:51:28 2021 +0000
@@ -30,7 +30,7 @@
   <inputs>
       <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."/>
-      <param name="iml_input" type="data" format="iml_dataset" 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="Dataset input" optional="true" help="This field accepts an ImmuneML dataset, as created by the Create Dataset tool."/>
   </inputs>
     <outputs>
         <data format="zip" name="optimal_model" label="optimal_ml_settings.zip"/>
--- a/immuneml_train_recept.xml	Thu Jul 01 14:43:41 2021 +0000
+++ b/immuneml_train_recept.xml	Thu Jul 01 16:51:28 2021 +0000
@@ -50,7 +50,7 @@
       ]]>
 </command>
     <inputs>
-        <param name="iml_input" type="data" format="iml_dataset" 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="Input 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	Thu Jul 01 14:43:41 2021 +0000
+++ b/immuneml_train_repert.xml	Thu Jul 01 16:51:28 2021 +0000
@@ -57,7 +57,7 @@
       ]]>
 </command>
     <inputs>
-        <param name="iml_input" type="data" format="iml_dataset"  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="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 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	Thu Jul 01 14:43:41 2021 +0000
+++ b/immuneml_yaml.xml	Thu Jul 01 16:51:28 2021 +0000
@@ -30,7 +30,7 @@
   <inputs>
       <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."/>
-      <param name="iml_input" type="data"  format="iml_dataset" 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."/>
   </inputs>
     <outputs>
         <data format="zip" name="archive" label="Archive: immuneML Analysis"/>