- This Markdown document will be used to generate your Galaxy Page. - This Markdown document will be used to generate your workflow invocation report. - This document should be Markdown with embedded commands for extracting and displaying Galaxy objects - and/or their metadata. -
++ This Markdown document will be used to generate your Galaxy Page. + This Markdown document will be used to generate your workflow invocation report. + This document should be Markdown with embedded commands for extracting and displaying Galaxy objects and/or + their metadata. +
-- For an overview of standard Markdown visit the - commonmark.org tutorial. -
++ For an overview of standard Markdown visit the + commonmark.org tutorial. +
-- The Galaxy extensions to Markdown are represented as code blocks, these blocks start with the line - ```galaxy and end with the line ``` and have a command with arguments between these - lines. - - These arguments reference your Galaxy objects such as datasets, jobs, and workflows. - - - These arguments reference parts of your workflow such as steps, inputs, and outputs by label in the - middle. - -
++ The Galaxy extensions to Markdown are represented as code blocks, these blocks start with the line + ```galaxy and end with the line ``` and have a command with arguments between these lines. + + These arguments reference your Galaxy objects such as datasets, jobs, and workflows. + + + These arguments reference parts of your workflow such as steps, inputs, and outputs by label in the + middle. + +
-- These commands reference a dataset or dataset collection. For instance, the following examples would - display the dataset collection metadata and would embed a dataset into the document as an image. +
+ These commands reference a dataset or dataset collection. For instance, the following examples would display + the dataset collection metadata and would embed a dataset into the document as an image. - - These elements are referenced by object IDs used by the Galaxy API. The Markdown editor will let you - pick objects graphically but they will be embedded into the Markdown with these IDs. - + + These elements are referenced by object IDs used by the Galaxy API. The Markdown editor will let you + pick objects graphically but they will be embedded into the Markdown with these IDs. + - - These elements are referenced by input or output labels for the workflow. If a dataset or collection - you'd like to reference is not available for selection in the Markdown editor, be sure to assign a - label to the object in the workflow editor first. - -
+ + These elements are referenced by input or output labels for the workflow. If a dataset or collection + you'd like to reference is not available for selection in the Markdown editor, be sure to assign a label + to the object in the workflow editor first. + + -+```galaxy history_dataset_collection_display(history_dataset_collection_id=33b43b4e7093c91f) ```-+ > +```galaxy history_dataset_collection_display(output=mapped_bams) ```+ > -+```galaxy history_dataset_as_image(history_dataset_id=33b43b4e7093c91f) ```-+ > +```galaxy history_dataset_as_image(output=normalized_result_plot) ```+ > -+ - Workflow Commands
+Workflow Commands
-- These commands reference a workflow by an object ID. The following example would display a - representation of the workflow in the resulting Galaxy Page: -
-These commands reference the current workflow and do not require an input for the most part.
++ These commands reference a workflow by an object ID. The following example would display a representation of + the workflow in the resulting Galaxy Page: +
+These commands reference the current workflow and do not require an input for the most part.
-+```galaxy workflow_display(workflow_id=33b43b4e7093c91f>) ```-+ > +-```galaxy workflow_display() ``` -++ - Job Commands
+Job Commands
-- These commands reference a Galaxy job. For instance, the following example would show the job parameters - the job ID 33b43b4e7093c91f. -
-- These commands reference a Galaxy job or collection of jobs associated with a labeled step in the - workflow. For instance, the following example would show the job parameters for the step with the label - mapping. -
++ These commands reference a Galaxy job. For instance, the following example would show the job parameters the + job ID 33b43b4e7093c91f. +
++ These commands reference a Galaxy job or collection of jobs associated with a labeled step in the workflow. + For instance, the following example would show the job parameters for the step with the label + mapping. +
-+```galaxy job_parameters(job_id=33b43b4e7093c91f) ```-+ > +-```galaxy job_parameters(step=mapping) ``` -+-