Mercurial > repos > tduigou > seq_from_db
diff seq_form_db.xml @ 2:11a3752feb0a draft default tip
planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 7f5d8b62d749a0c41110cd9c04e0254e4fd44893-dirty
| author | tduigou |
|---|---|
| date | Wed, 15 Oct 2025 12:33:41 +0000 |
| parents | 7680420caf9f |
| children |
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--- a/seq_form_db.xml Wed Jul 23 09:44:50 2025 +0000 +++ b/seq_form_db.xml Wed Oct 15 12:33:41 2025 +0000 @@ -1,8 +1,8 @@ <tool id="seq_form_db" name="Get sequences Data From DB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> <description>Import fragment's data from an accessible DB and export it as .gb files</description> <macros> - <token name="@VERSION_SUFFIX@">1</token> - <token name="@TOOL_VERSION@">0.2.0</token> + <token name="@VERSION_SUFFIX@">2</token> + <token name="@TOOL_VERSION@">0.3.0</token> </macros> <requirements> <requirement type="package" version="2.2.3">pandas</requirement> @@ -25,6 +25,7 @@ --json_conf '$json_use.json_conf' #end if --output 'outdir' + --report '$report' ]]></command> <inputs> <param name="input" type="data" format="csv" label="Input CSV File" /> @@ -46,6 +47,7 @@ <collection name="output_gb" type="list" label="GenBank Files collection" > <discover_datasets pattern="(?P<name>.*).gb" format="genbank" directory="outdir" /> </collection> + <data name='report' format='txt' label='missing fragments' /> </outputs> <tests> <!--manual parameters--> @@ -121,6 +123,11 @@ </assert_contents> </element> </output_collection> + <output name='report'> + <assert_contents> + <has_n_lines n="0" /> + </assert_contents> + </output> </test> <!--JSON parameters--> <test> @@ -191,6 +198,96 @@ </assert_contents> </element> </output_collection> + <output name='report'> + <assert_contents> + <has_n_lines n="0" /> + </assert_contents> + </output> + </test> + <!--test missing fragments--> + <test> + <param name="input" value="test_missing_input.csv" /> + <conditional name="json_use"> + <param name='use_json_paramers' value='false' /> + <param name="table" value="sample" /> + <param name="sequence_column" value="sequence" /> + <param name="annotation_columns" value="annotation" /> + <param name="fragment_column" value="fragment" /> + <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" /> + </conditional> + <output_collection name="output_gb" type="list" count="12"> + <element name="part_A"> + <assert_contents> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_B"> + <assert_contents> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_C"> + <assert_contents> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_D"> + <assert_contents> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_E"> + <assert_contents> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_F"> + <assert_contents> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_G"> + <assert_contents> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_H"> + <assert_contents> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_I"> + <assert_contents> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_J"> + <assert_contents> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_K"> + <assert_contents> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_L"> + <assert_contents> + <has_n_lines min="10" /> + </assert_contents> + </element> + </output_collection> + <output name='report'> + <assert_contents> + <has_n_lines n="6" /> + <has_line_matching expression="ACP10001AaCbbBS" /> + <has_line_matching expression="NEW20001BbDccKT" /> + <has_line_matching expression="XYZ10003AaCbbBS" /> + <has_line_matching expression="CFP10002AaCbbBS" /> + <has_line_matching expression="ALT30005CcEddLM" /> + <has_line_matching expression="QWE10004AaCbbBS" /> + </assert_contents> + </output> </test> </tests>