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<p>Describe an output parameter of a workflow. The parameter must be
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connected to one or more parameters defined in the workflow that will
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provide the value of the output parameter.</p>
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<h3>Fields</h3><tableclass="table table-striped"><tr><th>field</th><th>type</th><th>required</th><th>description</th></tr><tr><td><code>type</code></td><td><ahref="#datatype">Datatype</a> | <ahref="#outputschema">OutputSchema</a> | array<<ahref="#datatype">Datatype</a> | <ahref="#outputschema">OutputSchema</a>></td><td>False</td><td><p>Specify valid types of data that may be assigned to this parameter.
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<h3>Fields</h3><tableclass="table table-striped"><tr><th>field</th><th>type</th><th>required</th><th>description</th></tr><tr><td><code>type</code></td><td><ahref="#datatype">Datatype</a> | <ahref="#outputschema">OutputSchema</a> | <ahref="#datatype">string</a> | array<<ahref="#datatype">Datatype</a> | <ahref="#outputschema">OutputSchema</a> | <ahref="#datatype">string</a>></td><td>False</td><td><p>Specify valid types of data that may be assigned to this parameter.
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<em>Inherited from <ahref="#parameter">Parameter</a></em></p>
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</td></tr><tr><td><code>label</code></td><td><ahref="#datatype">string</a></td><td>False</td><td><p>A short, human-readable label of this parameter object. <em>Inherited from <ahref="#parameter">Parameter</a></em></p>
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</td></tr><tr><td><code>description</code></td><td><ahref="#datatype">string</a></td><td>False</td><td><p>A long, human-readable description of this parameter object. <em>Inherited from <ahref="#parameter">Parameter</a></em></p>
@@ -804,10 +804,16 @@ <h1 id="runtime_environment">Runtime environment</h1><p>All files listed in the
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output directory</strong>.</p>
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<p>The initial current working directory when executing the tool must be the
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designated output directory.</p>
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<p>When executing the tool, the child process must not inherit environment
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variables from the parent process. The tool must execute in a new, empty
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environment, containing only environment variables defined by
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<ahref="#envvarrequirement">EnvVarRequirement</a>, the default environment of the
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Docker container specified in <ahref="#dockerrequirement">DockerRequirement</a> (if
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applicable), and <code>TMPDIR</code>.</p>
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<p>The <code>TMPDIR</code> environment variable must be set in the runtime environment to
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the <strong>designated temporary directory</strong>. Any files written to the
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designated temporary directory may be deleted by the workflow
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platform when the tool invocation is complete.</p>
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designated temporary directory may be deleted by the workflow platform when
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the tool invocation is complete.</p>
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<p>An implementation may forbid the tool from writing to any location in the
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runtime environment file system other than the designated temporary
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directory and designated output directory. An implementation may provide
<p>Referenced by <ahref="#commandlinetool">CommandLineTool.inputs</a></p>
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<p>An input parameter for a CommandLineTool.</p>
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<h3>Fields</h3><tableclass="table table-striped"><tr><th>field</th><th>type</th><th>required</th><th>description</th></tr><tr><td><code>type</code></td><td><ahref="#datatype">Datatype</a> | <ahref="#commandinputschema">CommandInputSchema</a> | array<<ahref="#datatype">Datatype</a> | <ahref="#commandinputschema">CommandInputSchema</a>></td><td>False</td><td><p>Specify valid types of data that may be assigned to this parameter.
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<h3>Fields</h3><tableclass="table table-striped"><tr><th>field</th><th>type</th><th>required</th><th>description</th></tr><tr><td><code>type</code></td><td><ahref="#datatype">Datatype</a> | <ahref="#commandinputschema">CommandInputSchema</a> | <ahref="#datatype">string</a> | array<<ahref="#datatype">Datatype</a> | <ahref="#commandinputschema">CommandInputSchema</a> | <ahref="#datatype">string</a>></td><td>False</td><td><p>Specify valid types of data that may be assigned to this parameter.
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<em>Inherited from <ahref="#parameter">Parameter</a></em></p>
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</td></tr><tr><td><code>label</code></td><td><ahref="#datatype">string</a></td><td>False</td><td><p>A short, human-readable label of this parameter object. <em>Inherited from <ahref="#parameter">Parameter</a></em></p>
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</td></tr><tr><td><code>description</code></td><td><ahref="#datatype">string</a></td><td>False</td><td><p>A long, human-readable description of this parameter object. <em>Inherited from <ahref="#parameter">Parameter</a></em></p>
<p>Referenced by <ahref="#commandlinetool">CommandLineTool.outputs</a></p>
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<p>An output parameter for a CommandLineTool.</p>
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<h3>Fields</h3><tableclass="table table-striped"><tr><th>field</th><th>type</th><th>required</th><th>description</th></tr><tr><td><code>type</code></td><td><ahref="#datatype">Datatype</a> | <ahref="#commandoutputschema">CommandOutputSchema</a> | array<<ahref="#datatype">Datatype</a> | <ahref="#commandoutputschema">CommandOutputSchema</a>></td><td>False</td><td><p>Specify valid types of data that may be assigned to this parameter.
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<h3>Fields</h3><tableclass="table table-striped"><tr><th>field</th><th>type</th><th>required</th><th>description</th></tr><tr><td><code>type</code></td><td><ahref="#datatype">Datatype</a> | <ahref="#commandoutputschema">CommandOutputSchema</a> | <ahref="#datatype">string</a> | array<<ahref="#datatype">Datatype</a> | <ahref="#commandoutputschema">CommandOutputSchema</a> | <ahref="#datatype">string</a>></td><td>False</td><td><p>Specify valid types of data that may be assigned to this parameter.
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<em>Inherited from <ahref="#parameter">Parameter</a></em></p>
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</td></tr><tr><td><code>label</code></td><td><ahref="#datatype">string</a></td><td>False</td><td><p>A short, human-readable label of this parameter object. <em>Inherited from <ahref="#parameter">Parameter</a></em></p>
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</td></tr><tr><td><code>description</code></td><td><ahref="#datatype">string</a></td><td>False</td><td><p>A long, human-readable description of this parameter object. <em>Inherited from <ahref="#parameter">Parameter</a></em></p>
</td></tr><tr><td><code>description</code></td><td><ahref="#datatype">string</a></td><td>False</td><td><p>A long, human-readable description of this process object.</p>
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</td></tr></table><h1id="parameter">5.7.1 Parameter</h1><p>Extended by <ahref="#inputparameter">InputParameter</a>, <ahref="#outputparameter">OutputParameter</a></p>
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<p>Define an input or output parameter to a process.</p>
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<h3>Fields</h3><tableclass="table table-striped"><tr><th>field</th><th>type</th><th>required</th><th>description</th></tr><tr><td><code>type</code></td><td><ahref="#datatype">Datatype</a> | <ahref="#schema">Schema</a> | array<<ahref="#datatype">Datatype</a> | <ahref="#schema">Schema</a>></td><td>False</td><td><p>Specify valid types of data that may be assigned to this parameter.</p>
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<h3>Fields</h3><tableclass="table table-striped"><tr><th>field</th><th>type</th><th>required</th><th>description</th></tr><tr><td><code>type</code></td><td><ahref="#datatype">Datatype</a> | <ahref="#schema">Schema</a> | <ahref="#datatype">string</a> | array<<ahref="#datatype">Datatype</a> | <ahref="#schema">Schema</a> | <ahref="#datatype">string</a>></td><td>False</td><td><p>Specify valid types of data that may be assigned to this parameter.</p>
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</td></tr><tr><td><code>label</code></td><td><ahref="#datatype">string</a></td><td>False</td><td><p>A short, human-readable label of this parameter object.</p>
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</td></tr><tr><td><code>description</code></td><td><ahref="#datatype">string</a></td><td>False</td><td><p>A long, human-readable description of this parameter object.</p>
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</td></tr><tr><td><code>streamable</code></td><td><ahref="#datatype">boolean</a></td><td>False</td><td><p>Currently only applies if <code>type</code> is <code>File</code>. A value of <code>true</code>
<p>Extended by <ahref="#commandinputparameter">CommandInputParameter</a></p>
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<p>Referenced by <ahref="#process">Process.inputs</a>, <ahref="#expressiontool">ExpressionTool.inputs</a>, <ahref="#workflow">Workflow.inputs</a></p>
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<h3>Fields</h3><tableclass="table table-striped"><tr><th>field</th><th>type</th><th>required</th><th>description</th></tr><tr><td><code>type</code></td><td><ahref="#datatype">Datatype</a> | <ahref="#inputschema">InputSchema</a> | array<<ahref="#datatype">Datatype</a> | <ahref="#inputschema">InputSchema</a>></td><td>False</td><td><p>Specify valid types of data that may be assigned to this parameter.
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<h3>Fields</h3><tableclass="table table-striped"><tr><th>field</th><th>type</th><th>required</th><th>description</th></tr><tr><td><code>type</code></td><td><ahref="#datatype">Datatype</a> | <ahref="#inputschema">InputSchema</a> | <ahref="#datatype">string</a> | array<<ahref="#datatype">Datatype</a> | <ahref="#inputschema">InputSchema</a> | <ahref="#datatype">string</a>></td><td>False</td><td><p>Specify valid types of data that may be assigned to this parameter.
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<em>Inherited from <ahref="#parameter">Parameter</a></em></p>
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</td></tr><tr><td><code>label</code></td><td><ahref="#datatype">string</a></td><td>False</td><td><p>A short, human-readable label of this parameter object. <em>Inherited from <ahref="#parameter">Parameter</a></em></p>
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</td></tr><tr><td><code>description</code></td><td><ahref="#datatype">string</a></td><td>False</td><td><p>A long, human-readable description of this parameter object. <em>Inherited from <ahref="#parameter">Parameter</a></em></p>
<p>Extended by <ahref="#commandoutputparameter">CommandOutputParameter</a>, <ahref="#workflowoutputparameter">WorkflowOutputParameter</a></p>
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<p>Referenced by <ahref="#process">Process.outputs</a>, <ahref="#expressiontool">ExpressionTool.outputs</a></p>
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<h3>Fields</h3><tableclass="table table-striped"><tr><th>field</th><th>type</th><th>required</th><th>description</th></tr><tr><td><code>type</code></td><td><ahref="#datatype">Datatype</a> | <ahref="#outputschema">OutputSchema</a> | array<<ahref="#datatype">Datatype</a> | <ahref="#outputschema">OutputSchema</a>></td><td>False</td><td><p>Specify valid types of data that may be assigned to this parameter.
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<h3>Fields</h3><tableclass="table table-striped"><tr><th>field</th><th>type</th><th>required</th><th>description</th></tr><tr><td><code>type</code></td><td><ahref="#datatype">Datatype</a> | <ahref="#outputschema">OutputSchema</a> | <ahref="#datatype">string</a> | array<<ahref="#datatype">Datatype</a> | <ahref="#outputschema">OutputSchema</a> | <ahref="#datatype">string</a>></td><td>False</td><td><p>Specify valid types of data that may be assigned to this parameter.
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<em>Inherited from <ahref="#parameter">Parameter</a></em></p>
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</td></tr><tr><td><code>label</code></td><td><ahref="#datatype">string</a></td><td>False</td><td><p>A short, human-readable label of this parameter object. <em>Inherited from <ahref="#parameter">Parameter</a></em></p>
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</td></tr><tr><td><code>description</code></td><td><ahref="#datatype">string</a></td><td>False</td><td><p>A long, human-readable description of this parameter object. <em>Inherited from <ahref="#parameter">Parameter</a></em></p>
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