From a8c16060c1a15f5109d46a10ca36d0e9dbad1597 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 28 Aug 2024 17:32:31 -0400 Subject: [PATCH 1/3] Creation of FAQ for using workflow variables to rename outputs --- faqs/galaxy/workflows_variables.md | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 faqs/galaxy/workflows_variables.md diff --git a/faqs/galaxy/workflows_variables.md b/faqs/galaxy/workflows_variables.md new file mode 100644 index 00000000000000..3b3f27b98a8e8b --- /dev/null +++ b/faqs/galaxy/workflows_variables.md @@ -0,0 +1,25 @@ +--- +title: Rename outputs in a workflow using workflow variables +area: workflows +box_type: tip +layout: faq +contributors: [delphine-l] +--- + +Workflow text inputs can be used as parameters for tools but also in the workflow editor for renaming files. + +# Create a workflow variable + +1. Open the workflow editor +2. Click on **Inputs** in the toolbar on the left +3. Click on **Simple inputs used for Workflow logic** +4. Click on the created input box in the workflow editor +5. Label your input. Example: `Species Name` + +# Use a workflow variable to rename a dataset + +To use the workflow parameter for renaming a dataset, use the syntax: `${Parameter Name}`. For example, to rename a dataset using my species name: +1. Open the workflow editor +2. Click on the tool in the workflow to get the details of the tool on the right-hand side of the screen +3. Scroll down and click on **Configure Output** +4. In **Rename Dataset**, enter the new dataset name: `Tool run on ${Species Name}` \ No newline at end of file From 2a76b3e87cd7ab2f02373296e68fe3849dfe1e58 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 11 Sep 2024 15:39:43 -0400 Subject: [PATCH 2/3] Apply suggestions from Bjorn MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- faqs/galaxy/workflows_variables.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/faqs/galaxy/workflows_variables.md b/faqs/galaxy/workflows_variables.md index 3b3f27b98a8e8b..eacf2edf68d1f4 100644 --- a/faqs/galaxy/workflows_variables.md +++ b/faqs/galaxy/workflows_variables.md @@ -18,8 +18,8 @@ Workflow text inputs can be used as parameters for tools but also in the workflo # Use a workflow variable to rename a dataset -To use the workflow parameter for renaming a dataset, use the syntax: `${Parameter Name}`. For example, to rename a dataset using my species name: +To use the workflow parameter for renaming a dataset, use the syntax: `${Parameter Name}`. For example, to rename a dataset using the species name, proceed with the following steps: 1. Open the workflow editor -2. Click on the tool in the workflow to get the details of the tool on the right-hand side of the screen +2. Click on the tool in the workflow. This will open the tool configuration on the right-hand side of the screen with all details, like parameters etc. 3. Scroll down and click on **Configure Output** -4. In **Rename Dataset**, enter the new dataset name: `Tool run on ${Species Name}` \ No newline at end of file +4. In **Rename Dataset**, enter the new dataset name: `Tool run on ${Species Name}`. `Species Name` must match the workflow variable name you created before. \ No newline at end of file From 55f85d41f4f3b1a5e1ab4441990956b74b3fe957 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 11 Sep 2024 16:16:52 -0400 Subject: [PATCH 3/3] add the option to provide a variable name for the snippet --- faqs/galaxy/workflows_variables.md | 28 +++++++++++++++++++++++++++- 1 file changed, 27 insertions(+), 1 deletion(-) diff --git a/faqs/galaxy/workflows_variables.md b/faqs/galaxy/workflows_variables.md index eacf2edf68d1f4..4d4af659031269 100644 --- a/faqs/galaxy/workflows_variables.md +++ b/faqs/galaxy/workflows_variables.md @@ -4,10 +4,34 @@ area: workflows box_type: tip layout: faq contributors: [delphine-l] +optional_parameters: + var_name: Name of the workflow Variable +examples: + Use a Species Name: + var_name: "Species Name" --- Workflow text inputs can be used as parameters for tools but also in the workflow editor for renaming files. +{% if include.var_name %} +# Create a workflow variable + +1. Open the workflow editor +2. Click on **Inputs** in the toolbar on the left +3. Click on **Simple inputs used for Workflow logic** +4. Click on the created input box in the workflow editor +5. Label your input with `{{ include.var_name }}` + +# Use a workflow variable to rename a dataset + +To use the workflow parameter for renaming a dataset, use the syntax: `${Parameter Name}`. For example, to rename a dataset using the variable used above, proceed with the following steps: +1. Open the workflow editor +2. Click on the tool in the workflow. This will open the tool configuration on the right-hand side of the screen with all details, like parameters etc. +3. Scroll down and click on **Configure Output** +4. In **Rename Dataset**, enter the new dataset name: `Tool run on ${{{ include.var_name }}}`. `Species Name` must match the workflow variable name you created before. + +{% else %} + # Create a workflow variable 1. Open the workflow editor @@ -22,4 +46,6 @@ To use the workflow parameter for renaming a dataset, use the syntax: `${Paramet 1. Open the workflow editor 2. Click on the tool in the workflow. This will open the tool configuration on the right-hand side of the screen with all details, like parameters etc. 3. Scroll down and click on **Configure Output** -4. In **Rename Dataset**, enter the new dataset name: `Tool run on ${Species Name}`. `Species Name` must match the workflow variable name you created before. \ No newline at end of file +4. In **Rename Dataset**, enter the new dataset name: `Tool run on ${Species Name}`. `Species Name` must match the workflow variable name you created before. + +{% endif %} \ No newline at end of file