removed title parameter from templates and defined it in the "doc" pl…

…ugin" [#7]

etc/config

@@ -1,5 +1,6 @@
 plugins:
 - fileset
+- doc
 - configure
 - newjob
 - logger

lib/python/moa/plugin/doc.py

@@ -20,6 +20,20 @@
 import moa.utils
 import moa.logger as l
 
+def prepare(data):
+    job = data['job']
+
+    job.template.parameters.title = {
+        'optional' : False,
+        'help' : 'A short title for this job',
+        'type' : 'string'
+        }
+    job.template.parameters.project = {
+        'optional' : True,
+        'help' : 'Project name',
+        'type' : 'string'
+        }
+
 def defineCommands(data):
     """
     Set the moa commands for this plugin

template2/act_crunch.moa

@@ -56,11 +56,4 @@ parameters:
     help: Are we looking at proteins?
     optional: true
     type: set
-  title:
-    allowed: []
-    category: system
-    default: ''
-    help: A name for this job
-    optional: false
-    type: string
 title: Bidirectional best BLAST hit

template2/adhoc.moa

@@ -9,7 +9,8 @@ commands:
     help: ''
     mode: map
 creation_date: Wed Nov 10 07:56:48 2010
-description: The `adhoc` template assists in running one-liners - possibly on a set of input files
+description: The `adhoc` template assists in running one-liners - possibly on a set
+  of input files
 filesets:
   input:
     category: input
@@ -66,13 +67,6 @@ parameters:
       for example "cat $< > output" would concatenate all files into one big file
     optional: true
     type: string
-  title:
-    allowed: []
-    category: system
-    default: ''
-    help: A name for this job
-    optional: true
-    type: string
   touch:
     allowed:
     - T

template2/adhoc2.moa

@@ -1,14 +1,14 @@
 author: Mark Fiers
 backend: ruff
 commands:
-  runmap: 
+  runmap:
     help: ''
     mode: map
   runsimple:
     help: ''
     mode: simple
 creation_date: Wed Nov 10 07:56:48 2010
-description: The adhoc2 template aids in executing a one line on a set of input files. 
+description: The adhoc2 template aids in executing a one line on a set of input files.
 filesets:
   input:
     category: input
@@ -21,7 +21,7 @@ filesets:
     help: adhoc output files
     optional: true
     pattern: '*/*'
-    type: map    
+    type: map
 moa_id: adhoc2
 modification_date: Wed Nov 10 07:56:48 2010
 name: adhoc2
@@ -38,11 +38,4 @@ parameters:
       for example "cat $< > output" would concatenate all files into one big file
     optional: false
     type: string
-  title:
-    allowed: []
-    category: system
-    default: ''
-    help: A name for this job
-    optional: true
-    type: string
 title: Execute an ad hoc analysis

template2/adhoc_one.moa

@@ -26,11 +26,4 @@ parameters:
     help: The one-liner to execute
     optional: false
     type: string
-  title:
-    allowed: []
-    category: system
-    default: ''
-    help: A name for this job
-    optional: false
-    type: string
 title: Run an ad-hoc onliner

template2/bamextract.moa

@@ -54,11 +54,4 @@ parameters:
     help: List of sequence ids to extract
     optional: false
     type: string
-  title:
-    allowed: []
-    category: system
-    default: ''
-    help: A name for this job
-    optional: false
-    type: string
 title: Bamextract

template2/bartab.moa

@@ -75,13 +75,6 @@ parameters:
     help: remove reverse primer
     optional: true
     type: string
-  title:
-    allowed: []
-    category: system
-    default: ''
-    help: A name for this job
-    optional: false
-    type: string
   trim:
     allowed:
     - T

template2/bfast_aln.moa

@@ -22,14 +22,14 @@ filesets:
     optional: false
     pattern: '*/*.fq'
     type: set
-  output_bam:
+  output_aln:
     category: output
-    pattern: ./*.bam
+    pattern: ./*.aln
     source: fq_input
     type: map
-  output_aln:
+  output_bam:
     category: output
-    pattern: ./*.aln
+    pattern: ./*.bam
     source: fq_input
     type: map
 moa_id: bfast_aln
@@ -47,116 +47,110 @@ parameters:
     help: true -> colour space, false -> NT space
     optional: true
     type: boolean
-  timing_information:
+  avg_mism_qual:
     category: ''
-    default: true
-    help: specifies output timing information
+    default: 10
+    help: Specifies the average mismatch quality
     optional: true
-    type: boolean
-  print_params:
+    type: integer
+  extra_params_localalign:
+    allowed: []
     category: ''
-    default: false
-    help: print program parameters
+    default: ''
+    help: Any extra parameters for the localalign command
     optional: true
-    type: boolean
-  usage_summary:
+    type: string
+  extra_params_match:
+    allowed: []
     category: ''
-    default: false
-    help: Display usage summary (help)
+    default: ''
+    help: Any extra parameters for the match command
     optional: true
-    type: boolean
-  ungapped_aln:
+    type: string
+  extra_params_postprocess:
+    allowed: []
     category: ''
-    default: false
-    help: Do ungapped local alignment
+    default: ''
+    help: Any extra parameters for the postprocess command
     optional: true
-    type: boolean
-  unpaired_reads:
+    type: string
+  min_mapping_qual:
     category: ''
-    default: false
-    help: True value specifies that pairing should not be performed
+    default: -2147483648
+    help: Specifies to remove low mapping quality alignments
     optional: true
-    type: boolean
+    type: integer
+  min_norm_score:
+    category: ''
+    default: -2147483648
+    help: Specifies to remove low (alignment) scoring alignments
+    optional: true
+    type: integer
+  output_format:
+    category: ''
+    default: 1
+    help: 0 - BAF, 1 - SAM
+    optional: true
+    type: integer
   paired_opp_strands:
     category: ''
     default: false
     help: Specifies that paired reads are on opposite strands
     optional: true
     type: boolean
-  ungapped_pairing_rescue:
+  pairing_std_dev:
+    category: ''
+    default: 2.0
+    help: Specifies the pairing distance standard deviation to examine when recuing
+    optional: true
+    type: float
+  print_params:
     category: ''
     default: false
-    help: Specifies that ungapped pairing rescue should be performed
+    help: print program parameters
     optional: true
     type: boolean
   thread_num:
     category: ''
     default: 1
     help: Specifies the number of threads to use
     optional: true
-    type: integer 
-  avg_mism_qual:
-    category: ''
-    default: 10
-    help: Specifies the average mismatch quality
-    optional: true
-    type: integer 
-  min_mapping_qual:
-    category: ''
-    default: -2147483648
-    help: Specifies to remove low mapping quality alignments
-    optional: true
-    type: integer 
-  min_norm_score:
+    type: integer
+  timing_information:
     category: ''
-    default: -2147483648
-    help: Specifies to remove low (alignment) scoring alignments
+    default: true
+    help: specifies output timing information
     optional: true
-    type: integer 
-  pairing_std_dev:
+    type: boolean
+  ungapped_aln:
     category: ''
-    default: 2.000000
-    help: Specifies the pairing distance standard deviation to examine when recuing
+    default: false
+    help: Do ungapped local alignment
     optional: true
-    type: float
-  extra_params_match:
-    allowed: []
+    type: boolean
+  ungapped_pairing_rescue:
     category: ''
-    default: ''
-    help: Any extra parameters for the match command
+    default: false
+    help: Specifies that ungapped pairing rescue should be performed
     optional: true
-    type: string
-  extra_params_localalign:
-    allowed: []
+    type: boolean
+  unpaired_reads:
     category: ''
-    default: ''
-    help: Any extra parameters for the localalign command
+    default: false
+    help: True value specifies that pairing should not be performed
     optional: true
-    type: string
-  extra_params_postprocess:
-    allowed: []
+    type: boolean
+  usage_summary:
     category: ''
-    default: ''
-    help: Any extra parameters for the postprocess command
+    default: false
+    help: Display usage summary (help)
     optional: true
-    type: string
+    type: boolean
   which_strand:
     category: ''
     default: 0
-    help: 0 - consider both strands, 1 - forwards strand only, 2 - reverse strand only
-    optional: true
-    type: integer
-  output_format:
-    category: ''
-    default: 1
-    help: 0 - BAF, 1 - SAM
+    help: 0 - consider both strands, 1 - forwards strand only, 2 - reverse strand
+      only
     optional: true
     type: integer
-  title:
-    allowed: []
-    category: system
-    default: ''
-    help: A name for this job
-    optional: false
-    type: string
 version: 1