Mercurial > repos > siwaa > tabular_file_checker

changeset 0:9e72c0cef1f7 draft

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"planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
author siwaa
date Mon, 10 Jul 2023 14:15:29 +0000
parents
children fb2d0a0a55eb
files test-data/input/date.csv test-data/input/date_schema.json tfc.xml
diffstat 3 files changed, 71 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/date.csv	Mon Jul 10 14:15:29 2023 +0000
@@ -0,0 +1,6 @@
+dates, test
+2023-01-01, 2022-08-09
+2023-01-02, 2022-08-10
+2023-01-03, 2022-08-11
+2023-01-04, 2022-08-12
+2023-01-05, 2022-08-13
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/date_schema.json	Mon Jul 10 14:15:29 2023 +0000
@@ -0,0 +1,34 @@
+{
+    "name": "date",
+    "type": "table",
+    "path": "test-data/input/date.csv",
+    "scheme": "file",
+    "format": "csv",
+    "mediatype": "text/csv",
+    "encoding": "utf-8",
+    "hash": "sha256:4cfc5a1053f6cb741f7b5d7a59a5bf925b922f2ed59ff7b40a2b53db1e39e53c",
+    "bytes": 127,
+    "fields": 2,
+    "rows": 5,
+    "dialect": {
+        "csv": {
+            "skipInitialSpace": true
+        }
+    },
+    "schema": {
+        "fields": {
+            "dates": {
+                "type": "date",
+                "mandatory": false
+            },
+            "test": {
+                "type": "date",
+                "mandatory": false
+            }
+        }
+    },
+    "header": [
+        "dates",
+        "test"
+    ]
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tfc.xml	Mon Jul 10 14:15:29 2023 +0000
@@ -0,0 +1,31 @@
+<tool id="tfc" name="TabularFileChecker" version="1.0.0">
+  <description>to check tabular files content and structure</description>
+  <requirements>
+    <container type="singularity">docker://registry.forgemia.inra.fr/record/tfc:latest</container>
+  </requirements>
+  <command detect_errors="aggressive">
+    <![CDATA[
+             cp ${tabularInput} ./input.csv &&
+             tfc genschema genschema ./input.csv &&
+	     cp ./input*.json ${schema}
+     ]]>
+  </command>
+  <inputs>
+    <param name="tabularInput" type="data" format="csv" label="Select a csv file to check"/>
+  </inputs>
+  <outputs>
+    <data format="json" name="schema" label="${tabularInput.name} schema"/>
+  </outputs>
+  <tests>
+  </tests>
+  <help>
+Documentation
+-------------
+TODO
+
+Credits
+-------
+-  Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
+-  Copyright: INRAE
+  </help>
+</tool>