add awk process

zatsu_cwl_bioinformatics/2_awk.cwl

@@ -0,0 +1,35 @@
+#!/usr/bin/env cwl-runner
+# Generated from: awk '{ print  }' blastp_result.txt > blastp_result_id.txt
+class: CommandLineTool
+cwlVersion: v1.0
+baseCommand: awk
+arguments:
+  - $(inputs.'{)
+  - $(inputs.print)
+  - $(inputs.}')
+  - $(inputs.blastp_result_txt)
+inputs:
+  - id: '{
+    type: Any
+    default: '{
+  - id: print
+    type: Any
+    default: print
+  - id: }'
+    type: Any
+    default: }'
+  - id: blastp_result_txt
+    type: File
+    default:
+      class: File
+      location: blastp_result.txt
+outputs:
+  - id: all-for-debugging
+    type:
+      type: array
+      items: [File, Directory]
+    outputBinding:
+      glob: "*"
+  - id: out
+    type: stdout
+stdout: blastp_result_id.txt

zatsu_cwl_bioinformatics/2_awk_v2.cwl

@@ -0,0 +1,26 @@
+#!/usr/bin/env cwl-runner
+# Generated from: awk '{ print  }' blastp_result.txt > blastp_result_id.txt
+class: CommandLineTool
+cwlVersion: v1.0
+baseCommand: awk
+arguments: # argumentsを追加
+  - valueFrom: '{ print $2 }'
+    position: 1
+inputs:
+  - id: blastp_result
+    type: File
+    default:
+      class: File
+      location: ./blastp_result.txt
+    inputBinding:
+      position: 2 # positionを追加
+outputs:
+  - id: all-for-debugging
+    type:
+      type: array
+      items: [File, Directory]
+    outputBinding:
+      glob: "*"
+  - id: out
+    type: stdout
+stdout: blastp_result_id.txt

zatsu_cwl_bioinformatics/blastp_result.txt

@@ -1,8 +1,3 @@
-# BLASTP 2.2.31+
-# Query: sp|O18836|GDF8_BOVIN Growth/differentiation factor 8 OS=Bos taurus OX=9913 GN=MSTN PE=1 SV=2
-# Database: /var/lib/cwl/stg90d0f4dc-8137-4082-8c5d-4eaf670f8786/uniprot_sprot.fasta
-# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
-# 20 hits found
 sp|O18836|GDF8_BOVIN	sp|O18836|GDF8_BOVIN	100.00	375	0	0	1	375	1	375	0.0	783
 sp|O18836|GDF8_BOVIN	sp|Q5RZV4|GDF8_BOSIN	100.00	375	0	0	1	375	1	375	0.0	783
 sp|O18836|GDF8_BOVIN	sp|Q5USW1|GDF8_BOSGA	100.00	375	0	0	1	375	1	375	0.0	783
@@ -23,4 +18,3 @@ sp|O18836|GDF8_BOVIN	sp|O18828|GDF8_PAPHA	94.13	375	22	0	1	375	1	375	0.0	743
 sp|O18836|GDF8_BOVIN	sp|Q6UKZ8|GDF8_CANLF	93.33	375	25	0	1	375	1	375	0.0	741
 sp|O18836|GDF8_BOVIN	sp|Q5USV7|GDF8_AEPME	94.40	375	21	0	1	375	1	375	0.0	741
 sp|O18836|GDF8_BOVIN	sp|O18830|GDF8_SHEEP	93.33	375	25	0	1	375	1	375	0.0	738
-# BLAST processed 1 queries

zatsu_cwl_bioinformatics/blastp_result_id.txt

@@ -0,0 +1,20 @@
+sp|O18836|GDF8_BOVIN
+sp|Q5RZV4|GDF8_BOSIN
+sp|Q5USW1|GDF8_BOSGA
+sp|Q6X5V1|GDF8_BUBBU
+sp|Q5USW0|GDF8_TAUDE
+sp|O18831|GDF8_PIG
+sp|Q9GM97|GDF8_HORSE
+sp|Q5USV5|GDF8_ANTAM
+sp|A1C2U3|GDF8_PONPY
+sp|A1C2V0|GDF8_PANTR
+sp|A1C2U7|GDF8_PANPA
+sp|A1C2U6|GDF8_MACMU
+sp|Q95J86|GDF8_MACFA
+sp|A1C2V5|GDF8_GORGO
+sp|Q8HY52|GDF8_LEPCA
+sp|O14793|GDF8_HUMAN
+sp|O18828|GDF8_PAPHA
+sp|Q6UKZ8|GDF8_CANLF
+sp|Q5USV7|GDF8_AEPME
+sp|O18830|GDF8_SHEEP