minor work on templates

mfiers · Aug 3, 2012 · 7ff73b8 · 7ff73b8
1 parent 94f5140
commit 7ff73b8
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Showing 4 changed files with 40 additions and 26 deletions.
diff --git a/template2/bwa_aln.jinja2 b/template2/bwa_aln.jinja2
@@ -1,25 +1,25 @@
 ### run
 
 echo running bwa_aln
-bwa aln {{db}}                                                                  \
-	{% if edit_dist_missing_prob %} -n {{edit_dist_missing_prob}} {% endif %}   \
-    {% if gap_opens_max %} -o {{gap_opens_max}} {% endif %}                     \
-	{% if gap_ext_max %} -e {{gap_ext_max}} {% endif %}                         \
-    {% if no_indel_from_ends %} -i {{no_indel_from_ends}} {% endif %}           \
-	{% if max_ext_long_del %} -d {{max_ext_long_del}} {% endif %}               \
-	{% if seed_len %} -l {{seed_len}} {% endif %}                               \
-	{% if seed_max_diff %} -k {{seed_max_diff}} {% endif %}                     \
-	{% if max_queue_entry %} -m {{max_queue_entry}} {% endif %}                 \
-	{% if thread_num %} -t {{thread_num}} {% endif %}                           \
-	{% if mismatch_penalty %} -M {{mismatch_penalty}} {% endif %}               \
-	{% if gap_open_penalty %} -O {{gap_open_penalty}} {% endif %}               \
-	{% if gap_ext_penalty %} -E {{gap_ext_penalty}} {% endif %}                 \
-	{% if best_hits_stop %} -R {{best_hits_stop}} {% endif %}                   \
-	{% if quality_step %} -q {{quality_step}} {% endif %}                       \
-	{% if color_space %} -c {% endif %}                                         \
-	{% if log_gap_penalty_del %} -L {% endif %}	                                \
-	{% if non_iterative %} -N {% endif %}		                                \
-	{{ input }}									                                \
+bwa aln {{db}} \
+	{% if edit_dist_missing_prob %} -n {{edit_dist_missing_prob}} {% endif %} \
+    {% if gap_opens_max %} -o {{gap_opens_max}} {% endif %} \
+	{% if gap_ext_max %} -e {{gap_ext_max}} {% endif %} \
+    {% if no_indel_from_ends %} -i {{no_indel_from_ends}} {% endif %} \
+	{% if max_ext_long_del %} -d {{max_ext_long_del}} {% endif %} \
+	{% if seed_len %} -l {{seed_len}} {% endif %} \
+	{% if seed_max_diff %} -k {{seed_max_diff}} {% endif %} \
+	{% if max_queue_entry %} -m {{max_queue_entry}} {% endif %} \
+	{% if thread_num %} -t {{thread_num}} {% endif %} \
+	{% if mismatch_penalty %} -M {{mismatch_penalty}} {% endif %} \
+	{% if gap_open_penalty %} -O {{gap_open_penalty}} {% endif %} \
+	{% if gap_ext_penalty %} -E {{gap_ext_penalty}} {% endif %} \
+	{% if best_hits_stop %} -R {{best_hits_stop}} {% endif %} \
+	{% if quality_step %} -q {{quality_step}} {% endif %} \
+	{% if color_space %} -c {% endif %} \
+	{% if log_gap_penalty_del %} -L {% endif %} \
+	{% if non_iterative %} -N {% endif %} \
+	{{ input }} \
 	-f {{ output }}
 
 ### clean

diff --git a/template2/bwa_index.jinja2 b/template2/bwa_index.jinja2
@@ -1,10 +1,8 @@
 ### run 
 
-echo bwa index -p {{ prefix }} -a {{ algorithm }}               \
-     	{% if color_space %} -c {% endif %} {{ input }} 
-
-bwa index -p {{ prefix }} -a {{ algorithm }}                    \
-	{% if color_space %} -c {% endif %} {{ input }} 
+bwa index -p {{ prefix }} -a {{ algorithm }} \
+	{% if color_space %} -c {% endif %} \
+        {{ input }} 
 
 touch {{ prefix }}
 

diff --git a/template2/ncbi.moa b/template2/ncbi.moa
@@ -1,5 +1,8 @@
 author: Mark Fiers
 backend: ruff
+prerequisites:
+  xml_grep: 
+    version: 'xml_grep --version'
 commands:
   clean:
     help: Remove all job data, not the Moa job itself, note that this must be implemented
@@ -32,7 +35,7 @@ parameters:
     category: ''
     default: ''
     help: NCBI query (for example txid9397[Organism%3Aexp])
-    optional: true
+    optional: false
     type: string
   rename_sequence:
     default: false

diff --git a/template2/simple.jinja2 b/template2/simple.jinja2
@@ -5,7 +5,20 @@ echo '{{ process }}'
 
 
 ### unittest
+#!/bin/bash -v
+set -e
+tmpdir=`mktemp -d`
+cd $tmpdir
+touch 'testtesttest'
+moa new simple -t 'test'
+moa set title="helllloooooo!"
 
 moa set process=ls
-moa run
+echo '---------'
+cat .moa/config
+pwd
+ls -al
+moa
+moa run | grep 'testtesttest'
+rm -rf $tmpdir