Mercurial > repos > iuc > ragtag
diff ragtag.xml @ 2:b3c3217c0cbc draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675
| author | iuc |
|---|---|
| date | Fri, 14 Oct 2022 13:35:18 +0000 |
| parents | d110a4141898 |
| children |
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--- a/ragtag.xml Thu Jun 23 17:28:50 2022 +0000 +++ b/ragtag.xml Fri Oct 14 13:35:18 2022 +0000 @@ -236,7 +236,7 @@ </when> <when value="merge"> <param name="assembly_fasta" type="data" format="fasta" label="Assembly FASTA file"/> - <param name="scaffold_files" type="data" format="agp" multiple="true" optional="true" label="Scaffold AGP files"/> + <param name="scaffold_files" type="data" format="agp" multiple="true" min="2" label="Scaffold AGP files" help="At least two AGP files are required."/> <section name="merging_options" title="Merging options"> <param argument="-j" type="data" format="txt" optional="true" label="List of query headers to leave unplaced"/> <param argument="-l" type="integer" min="0" value="100000" label="Minimum assembly sequence length" @@ -272,63 +272,63 @@ </inputs> <outputs> <!--Correct mode outputs--> - <data format="paf" name="correct_paf" from_work_dir="ragtag.correct.asm.paf" label="${tool.name} on ${on_string}: PAF"> + <data format="paf" name="correct_paf" from_work_dir="ragtag.correct.asm.paf" label="${tool.name} on ${on_string}: correct PAF"> <filter>mode_conditional["mode_option"] == "correct" and "paf" in mode_conditional["output_correct"]</filter> </data> - <data format="agp" name="correct_agp" from_work_dir="ragtag.correct.agp" label="${tool.name} on ${on_string}: AGP"> + <data format="agp" name="correct_agp" from_work_dir="ragtag.correct.agp" label="${tool.name} on ${on_string}: correct AGP"> <filter>mode_conditional["mode_option"] == "correct" and "agp" in mode_conditional["output_correct"]</filter> </data> - <data format="fasta" name="correct_fasta" from_work_dir="ragtag.correct.fasta" label="${tool.name} on ${on_string}: FASTA"> + <data format="fasta" name="correct_fasta" from_work_dir="ragtag.correct.fasta" label="${tool.name} on ${on_string}: correct FASTA"> <filter>mode_conditional["mode_option"] == "correct" and "fasta" in mode_conditional["output_correct"]</filter> </data> - <data format="txt" name="correct_log" from_work_dir="ragtag.correct.asm.paf.log" label="${tool.name} on ${on_string}: log"> + <data format="txt" name="correct_log" from_work_dir="ragtag.correct.asm.paf.log" label="${tool.name} on ${on_string}: correct log"> <filter>mode_conditional["mode_option"] == "correct" and "log" in mode_conditional["output_correct"]</filter> </data> <!--Scaffold mode outputs--> - <data format="paf" name="scaffold_paf" from_work_dir="ragtag.scaffold.asm.paf" label="${tool.name} on ${on_string}: PAF"> + <data format="paf" name="scaffold_paf" from_work_dir="ragtag.scaffold.asm.paf" label="${tool.name} on ${on_string}: scaffold PAF"> <filter>mode_conditional["mode_option"] == "scaffold" and "paf" in mode_conditional["output_scaffold"]</filter> </data> - <data format="agp" name="scaffold_agp" from_work_dir="ragtag.scaffold.agp" label="${tool.name} on ${on_string}: AGP"> + <data format="agp" name="scaffold_agp" from_work_dir="ragtag.scaffold.agp" label="${tool.name} on ${on_string}: scaffold AGP"> <filter>mode_conditional["mode_option"] == "scaffold" and "agp" in mode_conditional["output_scaffold"]</filter> </data> - <data format="fasta" name="scaffold_fasta" from_work_dir="ragtag.scaffold.fasta" label="${tool.name} on ${on_string}: FASTA"> + <data format="fasta" name="scaffold_fasta" from_work_dir="ragtag.scaffold.fasta" label="${tool.name} on ${on_string}: scaffold FASTA"> <filter>mode_conditional["mode_option"] == "scaffold" and "fasta" in mode_conditional["output_scaffold"]</filter> </data> - <data format="txt" name="scaffold_log" from_work_dir="ragtag.scaffold.asm.paf.log" label="${tool.name} on ${on_string}: log"> + <data format="txt" name="scaffold_log" from_work_dir="ragtag.scaffold.asm.paf.log" label="${tool.name} on ${on_string}: scaffold log"> <filter>mode_conditional["mode_option"] == "scaffold" and "log" in mode_conditional["output_scaffold"]</filter> </data> - <data format="tabular" name="scaffold_stats" from_work_dir="ragtag.scaffold.stats" label="${tool.name} on ${on_string}: stats"> + <data format="tabular" name="scaffold_stats" from_work_dir="ragtag.scaffold.stats" label="${tool.name} on ${on_string}: scaffold stats"> <filter>mode_conditional["mode_option"] == "scaffold" and "stats" in mode_conditional["output_scaffold"]</filter> </data> - <data format="tabular" name="scaffold_confidence" from_work_dir="ragtag.scaffold.confidence.txt" label="${tool.name} on ${on_string}: confidence"> + <data format="tabular" name="scaffold_confidence" from_work_dir="ragtag.scaffold.confidence.txt" label="${tool.name} on ${on_string}: scaffold confidence"> <filter>mode_conditional["mode_option"] == "scaffold" and "confidence" in mode_conditional["output_scaffold"]</filter> </data> <!--Patch mode outputs--> - <data format="agp" name="patch_agp" from_work_dir="ragtag.patch.agp" label="${tool.name} on ${on_string}: final AGP"> + <data format="agp" name="patch_agp" from_work_dir="ragtag.patch.agp" label="${tool.name} on ${on_string}: patch final AGP"> <filter>mode_conditional["mode_option"] == "patch" and "final_agp" in mode_conditional["output_patch"]</filter> </data> - <data format="paf" name="patch_paf" from_work_dir="ragtag.patch.asm.paf" label="${tool.name} on ${on_string}: final PAF"> + <data format="paf" name="patch_paf" from_work_dir="ragtag.patch.asm.paf" label="${tool.name} on ${on_string}: patch final PAF"> <filter>mode_conditional["mode_option"] == "patch" and "assembly_file" in mode_conditional["output_patch"]</filter> </data> - <data format="txt" name="patch_log" from_work_dir="ragtag.patch.log" label="${tool.name} on ${on_string}: log"> + <data format="txt" name="patch_log" from_work_dir="ragtag.patch.log" label="${tool.name} on ${on_string}: patch log"> <filter>mode_conditional["mode_option"] == "patch" and "log" in mode_conditional["output_patch"]</filter> </data> - <data format="fasta" name="patch_comps_fasta" from_work_dir="ragtag.patch.comps.fasta" label="${tool.name} on ${on_string}: components FASTA"> + <data format="fasta" name="patch_comps_fasta" from_work_dir="ragtag.patch.comps.fasta" label="${tool.name} on ${on_string}: patch components FASTA"> <filter>mode_conditional["mode_option"] == "patch" and "split_assembly" in mode_conditional["output_patch"]</filter> </data> - <data format="agp" name="patch_ctg_agp" from_work_dir="ragtag.patch.ctg.agp" label="${tool.name} on ${on_string}: contigs AGP"> + <data format="agp" name="patch_ctg_agp" from_work_dir="ragtag.patch.ctg.agp" label="${tool.name} on ${on_string}: patch contigs AGP"> <filter>mode_conditional["mode_option"] == "patch" and "split_description" in mode_conditional["output_patch"]</filter> </data> - <data format="fasta" name="patch_ctg_fasta" from_work_dir="ragtag.patch.ctg.fasta" label="${tool.name} on ${on_string}: contigs FASTA"> + <data format="fasta" name="patch_ctg_fasta" from_work_dir="ragtag.patch.ctg.fasta" label="${tool.name} on ${on_string}: patch contigs FASTA"> <filter>mode_conditional["mode_option"] == "patch" and "target_gaps" in mode_conditional["output_patch"]</filter> </data> - <data format="fasta" name="patch_fasta" from_work_dir="ragtag.patch.fasta" label="${tool.name} on ${on_string}: final FASTA"> + <data format="fasta" name="patch_fasta" from_work_dir="ragtag.patch.fasta" label="${tool.name} on ${on_string}: patch final FASTA"> <filter>mode_conditional["mode_option"] == "patch" and "final_fasta" in mode_conditional["output_patch"]</filter> </data> - <data format="agp" name="patch_rename_agp" from_work_dir="ragtag.patch.rename.agp" label="${tool.name} on ${on_string}: renamed AGP"> + <data format="agp" name="patch_rename_agp" from_work_dir="ragtag.patch.rename.agp" label="${tool.name} on ${on_string}: patch renamed AGP"> <filter>mode_conditional["mode_option"] == "patch" and "agp_renamed" in mode_conditional["output_patch"]</filter> </data> - <data format="fasta" name="patch_rename_fasta" from_work_dir="ragtag.patch.rename.fasta" label="${tool.name} on ${on_string}: renamed FASTA"> + <data format="fasta" name="patch_rename_fasta" from_work_dir="ragtag.patch.rename.fasta" label="${tool.name} on ${on_string}: patch renamed FASTA"> <filter>mode_conditional["mode_option"] == "patch" and "fasta_renamed" in mode_conditional["output_patch"]</filter> </data> <!-- Merge mode outputs--> @@ -549,4 +549,4 @@ ]]> </help> <expand macro="citations" /> -</tool> \ No newline at end of file +</tool>