Commit 339a12e1 authored by Peter Kruczkiewicz's avatar Peter Kruczkiewicz

enable post-assembly correction with PILON for asm/annt pipelines; add tool...

enable post-assembly correction with PILON for asm/annt pipelines; add tool param for shovill nocorr
parent 16aed941
Pipeline #7598 canceled with stage
......@@ -13,27 +13,30 @@
<parameter name="shovill-1-adv.mincov" defaultValue="2">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.mincov"/>
</parameter>
<parameter name="shovill-1-trim" defaultValue="false">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="trim"/>
</parameter>
<parameter name="shovill-1-adv.namefmt" defaultValue="contig%05d">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.namefmt"/>
</parameter>
<parameter name="shovill-1-adv.depth" defaultValue="100">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.depth"/>
</parameter>
<parameter name="shovill-1-nocorr" defaultValue="false">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="nocorr"/>
</parameter>
<parameter name="shovill-1-trim" defaultValue="false">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="trim"/>
</parameter>
<parameter name="shovill-1-adv.gsize" defaultValue="">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.gsize"/>
</parameter>
<parameter name="shovill-1-adv.kmers" defaultValue="">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.kmers"/>
</parameter>
<parameter name="shovill-1-adv.opts" defaultValue="">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.opts"/>
</parameter>
<parameter name="shovill-1-adv.minlen" defaultValue="0">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.minlen"/>
</parameter>
<parameter name="shovill-1-adv.namefmt" defaultValue="contig%05d">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.namefmt"/>
</parameter>
<parameter name="shovill-1-adv.opts" defaultValue="">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.opts"/>
</parameter>
<parameter name="quast-2-min_contig" defaultValue="500">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.6.3" parameterName="min_contig"/>
</parameter>
......
......@@ -97,7 +97,7 @@
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"adv\": \"{\\\"asm\\\": \\\"contigs\\\", \\\"gsize\\\": \\\"\\\", \\\"kmers\\\": \\\"\\\", \\\"minlen\\\": \\\"0\\\", \\\"nocorr\\\": \\\"true\\\", \\\"depth\\\": \\\"100\\\", \\\"namefmt\\\": \\\"contig%05d\\\", \\\"mincov\\\": \\\"2\\\", \\\"opts\\\": \\\"\\\"}\", \"trim\": \"\\\"false\\\"\", \"log\": \"\\\"true\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"lib_type\\\": \\\"collection\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\"}",
"tool_state": "{\"adv\": \"{\\\"asm\\\": \\\"contigs\\\", \\\"gsize\\\": \\\"\\\", \\\"kmers\\\": \\\"\\\", \\\"minlen\\\": \\\"0\\\", \\\"nocorr\\\": \\\"false\\\", \\\"depth\\\": \\\"100\\\", \\\"namefmt\\\": \\\"contig%05d\\\", \\\"mincov\\\": \\\"2\\\", \\\"opts\\\": \\\"\\\"}\", \"trim\": \"\\\"false\\\"\", \"log\": \"\\\"true\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"lib_type\\\": \\\"collection\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\"}",
"tool_version": "0.9.0",
"type": "tool",
"uuid": "b9b506b8-bedf-4d23-994a-25d45cdf0343",
......
......@@ -7,6 +7,7 @@ pipeline.parameters.modal-title.assemblyannotation=Assembly and Annotation Pipel
#Tool Parameters - Tool: shovill - Workflow Step #: 1
pipeline.parameters.assemblyannotation.shovill-1-adv.mincov=Shovill: Minimum coverage to call part of a contig. (0 is AUTO)
pipeline.parameters.assemblyannotation.shovill-1-nocorr=Shovill: Disable post-assembly correction with PILON?
pipeline.parameters.assemblyannotation.shovill-1-trim=Shovill: Use Trimmomatic to remove common adaptors first?
pipeline.parameters.assemblyannotation.shovill-1-adv.namefmt=Shovill: Format of output contig FASTA IDs in 'printf' style.
pipeline.parameters.assemblyannotation.shovill-1-adv.depth=Shovill: Sub-sample reads to specified depth (0 to disable sub-sampling)
......
......@@ -12,27 +12,30 @@
<parameter name="shovill-1-adv.mincov" defaultValue="2">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.mincov"/>
</parameter>
<parameter name="shovill-1-trim" defaultValue="false">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="trim"/>
</parameter>
<parameter name="shovill-1-adv.namefmt" defaultValue="contig%05d">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.namefmt"/>
</parameter>
<parameter name="shovill-1-adv.depth" defaultValue="100">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.depth"/>
</parameter>
<parameter name="shovill-1-nocorr" defaultValue="false">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="nocorr"/>
</parameter>
<parameter name="shovill-1-trim" defaultValue="false">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="trim"/>
</parameter>
<parameter name="shovill-1-adv.gsize" defaultValue="">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.gsize"/>
</parameter>
<parameter name="shovill-1-adv.kmers" defaultValue="">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.kmers"/>
</parameter>
<parameter name="shovill-1-adv.opts" defaultValue="">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.opts"/>
</parameter>
<parameter name="shovill-1-adv.minlen" defaultValue="0">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.minlen"/>
</parameter>
<parameter name="shovill-1-adv.namefmt" defaultValue="contig%05d">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.namefmt"/>
</parameter>
<parameter name="shovill-1-adv.opts" defaultValue="">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0" parameterName="adv.opts"/>
</parameter>
<parameter name="quast-2-min_contig" defaultValue="500">
<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.6.3" parameterName="min_contig"/>
</parameter>
......
......@@ -81,7 +81,7 @@
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"adv\": \"{\\\"asm\\\": \\\"contigs\\\", \\\"gsize\\\": \\\"\\\", \\\"kmers\\\": \\\"\\\", \\\"minlen\\\": \\\"0\\\", \\\"nocorr\\\": \\\"true\\\", \\\"depth\\\": \\\"100\\\", \\\"namefmt\\\": \\\"contig%05d\\\", \\\"mincov\\\": \\\"2\\\", \\\"opts\\\": \\\"\\\"}\", \"trim\": \"\\\"false\\\"\", \"log\": \"\\\"true\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"lib_type\\\": \\\"collection\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\"}",
"tool_state": "{\"adv\": \"{\\\"asm\\\": \\\"contigs\\\", \\\"gsize\\\": \\\"\\\", \\\"kmers\\\": \\\"\\\", \\\"minlen\\\": \\\"0\\\", \\\"nocorr\\\": \\\"false\\\", \\\"depth\\\": \\\"100\\\", \\\"namefmt\\\": \\\"contig%05d\\\", \\\"mincov\\\": \\\"2\\\", \\\"opts\\\": \\\"\\\"}\", \"trim\": \"\\\"false\\\"\", \"log\": \"\\\"true\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"lib_type\\\": \\\"collection\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\"}",
"tool_version": "0.9.0",
"type": "tool",
"uuid": "04e633cb-5bfc-4afd-935e-ee49cc18c6c4",
......
......@@ -7,6 +7,7 @@ workflow.assembly-annotation-collection.title=AssemblyAnnotationCollection Pipel
#Tool Parameters - Tool: shovill - Workflow Step #: 1
pipeline.parameters.assemblyannotationcollection.shovill-1-adv.mincov=Shovill: Minimum coverage to call part of a contig. (0 is AUTO)
pipeline.parameters.assemblyannotation.shovill-1-nocorr=Shovill: Disable post-assembly correction with PILON?
pipeline.parameters.assemblyannotationcollection.shovill-1-trim=Shovill: Use Trimmomatic to remove common adaptors first?
pipeline.parameters.assemblyannotationcollection.shovill-1-adv.namefmt=Shovill: Format of output contig FASTA IDs in 'printf' style.
pipeline.parameters.assemblyannotationcollection.shovill-1-adv.depth=Shovill: Sub-sample reads to specified depth (0 to disable sub-sampling)
......
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