From 9a88ef161fa266f3115536b39cab808fbf3f26f8 Mon Sep 17 00:00:00 2001
From: stamper <tbyhdgs@gmail.com>
Date: Sat, 27 Jul 2019 17:01:23 +0200
Subject: [PATCH 1/3] rough draft of Miscellaneous page

---
 _extras/miscellaneous.md | 130 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 130 insertions(+)
 create mode 100644 _extras/miscellaneous.md

diff --git a/_extras/miscellaneous.md b/_extras/miscellaneous.md
new file mode 100644
index 00000000..859bfe0c
--- /dev/null
+++ b/_extras/miscellaneous.md
@@ -0,0 +1,130 @@
+---
+layout: page
+title: Miscellaneous
+permalink: /misc/
+---
+
+This is a collection of examples and short notes
+about some operations that fall outside the scope of the User Guide
+and/or have not yet been implemented in a clean way in the CWL specification.
+
+### Get output values of a specific type using `evalFrom`
+
+```yaml
+cwlVersion: v1.0  # or v1.1
+class: CommandLineTool
+requirements:
+  InlineJavascriptRequirement: {}
+
+baseCommand: [ echo, "42" ]
+
+inputs: []
+
+stdout: my_number.txt
+
+outputs:
+  my_number:
+    type: int
+    outputBinding:
+       glob: my_number.txt
+       loadContents: True
+       outputEval: $(parselnt(self[0].contents))
+
+  my_number_as_string:
+    type: string
+    outputBinding:
+       glob: my_number.txt
+       loadContents: True
+       outputEval: $(self[0].contents)
+```
+
+### Rename an input file
+
+This example shows how you can change the name of an input file
+as part of a tool description.
+This could be useful when you are taking files produced from another
+step in a workflow and don't want to work with the default names that these
+files were given when they were created.
+
+```yaml
+requirements:
+  InitialWorkDirRequirement:
+    listing:
+      - entry: $(inputs.src1)
+        entryName: newName
+      - entry: $(inputs.src2)
+        entryName: $(inputs.src1.basename)_custom_extension
+```
+
+### Rename an output file
+
+This example shows how you can change the name an output file
+from the default name given to it by a tool:
+
+```yaml
+cwlVersion: v1.0 # or v1.1
+class: CommandLineTool
+requirements:
+  InlineJavascriptRequirement: {}
+
+baseCommand: []
+
+inputs: []
+
+outputs:
+ otu_table:
+    type: File
+    outputBinding:
+      glob: otu_table.txt
+      outputEval: ${self[0].basename=inputs.otu_table_name; return self;}
+```
+
+### Setting `self`-based input bindings for optional inputs
+
+Currently, `cwltool` can't cope with missing optional inputs if their
+input binding makes use of `self`.
+Below is an example workaround for this,
+pending a more sophisticated fix.
+
+```yaml
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements: { InlineJavascriptRequirement: {} }
+
+inputs:
+  cfg:
+    type: File?
+    inputBinding:
+      prefix: -cfg
+      valueFrom: |
+        ${ if(self === null) { return null;} else { return self.basename; } }
+
+baseCommand: echo
+
+outputs: []
+```
+
+### Model a "one-or-the-other" parameter
+
+Below is an example of how
+you can specify different strings to be added to a command line
+based on the value given to a Boolean parameter.
+
+```yaml
+cwlVersion: v1.0
+class: CommandLineTool
+requirements:
+  InlineJavascriptRequirement: {}
+inputs:
+  fancy_bool:
+     type: boolean
+     default: false  # or true
+     inputBinding:
+        valueFrom: ${if (self) { return "foo";} else { return "bar";}}
+
+baseCommand: echo
+
+outputs: []
+```

From 6171a38f65e31dc149d4f21860f6cc75d33e0f98 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com>
Date: Sat, 27 Jul 2019 17:12:21 +0200
Subject: [PATCH 2/3] standards

---
 _extras/miscellaneous.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/_extras/miscellaneous.md b/_extras/miscellaneous.md
index 859bfe0c..faacbb4d 100644
--- a/_extras/miscellaneous.md
+++ b/_extras/miscellaneous.md
@@ -6,7 +6,7 @@ permalink: /misc/
 
 This is a collection of examples and short notes
 about some operations that fall outside the scope of the User Guide
-and/or have not yet been implemented in a clean way in the CWL specification.
+and/or have not yet been implemented in a clean way in the CWL standards.
 
 ### Get output values of a specific type using `evalFrom`
 

From 88ea048239beafdc8960c6cc9cc51f74db586a29 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com>
Date: Sat, 27 Jul 2019 17:12:28 +0200
Subject: [PATCH 3/3] Update _extras/miscellaneous.md

---
 _extras/miscellaneous.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/_extras/miscellaneous.md b/_extras/miscellaneous.md
index faacbb4d..d2cb9062 100644
--- a/_extras/miscellaneous.md
+++ b/_extras/miscellaneous.md
@@ -8,7 +8,7 @@ This is a collection of examples and short notes
 about some operations that fall outside the scope of the User Guide
 and/or have not yet been implemented in a clean way in the CWL standards.
 
-### Get output values of a specific type using `evalFrom`
+### Non "`File`" types using `evalFrom`
 
 ```yaml
 cwlVersion: v1.0  # or v1.1