Merge pull request #420 from StanfordBioinformatics/documentation

Documentation

doc/about.rst

@@ -1,3 +1,7 @@
+#####
+About
+#####
+
 What is Loom?
 =============
 

doc/examples/add_then_multiply/add_then_multiply.yaml

@@ -0,0 +1,48 @@
+name: add_then_multiply
+inputs:
+  - type: integer
+    channel: a
+    data:
+      contents: 3
+  - type: integer
+    channel: b
+    data:
+      contents: 5
+  - type: integer
+    channel: c
+    data:
+      contents: 7
+outputs:
+  - type: integer
+    channel: result
+steps:
+  - name: add
+    command: print({{ a }} + {{ b }}, end='')
+    environment:
+      docker_image: python
+    interpreter: python
+    inputs:
+      - type: integer
+        channel: a
+      - type: integer
+        channel: b
+    outputs:
+      - type: integer
+        channel: ab_sum
+        source:
+          stream: stdout
+  - name: multiply
+    command: print({{ c }} * {{ ab_sum }}, end='')
+    environment:
+      docker_image: python
+    interpreter: python
+    inputs:
+      - type: integer
+        channel: ab_sum
+      - type: integer
+        channel: c
+    outputs:
+      - type: integer
+        channel: result
+        source:
+          stream: stdout

doc/examples/building_blocks/add.yaml

@@ -0,0 +1,15 @@
+name: add
+command: print({{ a }} + {{ b }}, end='')
+environment:
+  docker_image: python
+interpreter: python
+inputs:
+  - type: integer
+    channel: a
+  - type: integer
+    channel: b
+outputs:
+  - type: integer
+    channel: ab_sum
+    source:
+      stream: stdout

doc/examples/building_blocks/building_blocks.yaml

@@ -0,0 +1,20 @@
+name: building_blocks
+inputs:
+  - type: integer
+    channel: a
+    data:
+      contents: 3
+  - type: integer
+    channel: b
+    data:
+      contents: 5
+  - type: integer
+    channel: c
+    data:
+      contents: 7
+outputs:
+  - type: integer
+    channel: result
+steps:
+  - add$5b4c0b69984d50284d0a3c38f735c532
+  - multiply$32b277628f359b590304f69202cd6f86

doc/examples/building_blocks/multiply.yaml

@@ -0,0 +1,15 @@
+name: multiply
+command: print({{ c }} * {{ ab_sum }}, end='')
+environment:
+  docker_image: python
+interpreter: python
+inputs:
+  - type: integer
+    channel: ab_sum
+  - type: integer
+    channel: c
+outputs:
+  - type: integer
+    channel: result
+    source:
+      stream: stdout

doc/examples/capitalize_words/capitalize_words.yaml

@@ -0,0 +1,15 @@
+name: capitalize_words
+command: echo -n {{word}} | awk '{print toupper($0)}'
+environment:
+  docker_image: ubuntu:latest
+inputs:
+  - channel: words
+    as_channel: word
+    type: string
+    data:
+      contents: [aardvark,aback,abacus,abaft]
+outputs:
+  - channel: wordoutput
+    type: string
+    source:
+      stream: stdout

doc/examples/hello_world/hello_world.yaml

@@ -1,4 +1,3 @@
----
 name: hello_world
 inputs:
 - type: file

doc/examples/join_array_of_words/join_array_of_words.yaml

@@ -0,0 +1,15 @@
+name: join_array_of_words
+command: echo -n {{wordarray}}
+environment:
+  docker_image: ubuntu:latest
+inputs:
+  - channel: wordarray
+    type: string
+    mode: gather
+    data:
+      contents: [aardvark,aback,abacus,abaft]
+outputs:
+  - channel: wordoutput
+    type: string
+    source:
+      stream: stdout

doc/examples/join_two_words/join_two_words.yaml

@@ -0,0 +1,18 @@
+name: join_two_words
+command: echo {{word1}} {{word2}}
+environment:
+  docker_image: ubuntu:latest
+inputs:
+  - channel: word1
+    type: string
+    data:
+      contents: hello
+  - channel: word2
+    type: string
+    data:
+      contents: world
+outputs:
+  - channel: output_text
+    type: string
+    source:
+      stream: stdout

doc/examples/search_file/beowulf.txt

@@ -0,0 +1,13 @@
+Lo! the Spear-Danes' glory through splendid achievements
+The folk-kings' former fame we have heard of,
+How princes displayed then their prowess-in-battle.
+Oft Scyld the Scefing from scathers in numbers
+From many a people their mead-benches tore.
+Since first he found him friendless and wretched,
+The earl had had terror: comfort he got for it,
+Waxed 'neath the welkin, world-honor gained,
+Till all his neighbors o'er sea were compelled to
+Bow to his bidding and bring him their tribute:
+An excellent atheling! After was borne him
+A son and heir, young in his dwelling,
+Whom God-Father sent to solace the people.

doc/examples/search_file/lorem_ipsum.txt

@@ -0,0 +1,9 @@
+Lorem ipsum dolor sit amet, consectetur adipiscing
+elit, sed do eiusmod tempor incididunt ut labore et
+dolore magna aliqua. Ut enim ad minim veniam, quis
+nostrud exercitation ullamco laboris nisi ut aliquip
+ex ea commodo consequat. Duis aute irure dolor in
+reprehenderit in voluptate velit esse cillum dolore
+eu fugiat nulla pariatur. Excepteur sint occaecat
+cupidatat non proident, sunt in culpa qui officia
+deserunt mollit anim id est laborum.

doc/examples/search_file/search_file.yaml

@@ -0,0 +1,23 @@
+name: search_file
+command: grep {{pattern}} {{file_to_search}}
+environment:
+  docker_image: ubuntu:latest
+inputs:
+  - channel: file_to_search
+    type: file
+    data:
+      contents: lorem_ipsum.txt
+  - channel: pattern
+    type: string
+    data:
+      contents: dolor
+outputs:
+  - channel: matches
+    type: string
+    mode: scatter
+    source:
+      stream: stdout
+    parser:
+      type: delimited
+      options:
+        delimiter: "\n"