Mercurial > repos > bgruening > instagraal

changeset 2:d1be552c6034 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/instagraal commit c5ff906bec1f07b06a60081f7db3fc8f0c6e94b8
author bgruening
date Sun, 27 Aug 2023 09:28:26 +0000
parents 8d5b13b571fd
children
files instagraal.xml
diffstat 1 files changed, 14 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/instagraal.xml	Sun Nov 13 12:59:17 2022 +0000
+++ b/instagraal.xml	Sun Aug 27 09:28:26 2023 +0000
@@ -1,21 +1,25 @@
-<tool id="instagraal" name="instaGRAAL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="instagraal" name="instaGRAAL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
     <description>Large genome reassembly based on Hi-C data</description>
+    <xrefs>
+        <xref type="bio.tools">instagraal</xref>
+    </xrefs>
     <macros>
         <token name="@TOOL_VERSION@">0.1.6</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
-    <xrefs>
-        <xref type="bio.tools">instagraal</xref>
-    </xrefs>
+    <requirements>
+        <!-- use a versioned copy of the upstream container at koszullab/instagraal -->
+        <container type="docker">quay.io/galaxy/instagraal:0.1.6</container>
+        <resource type="cuda_version_min">10.0</resource>
+        <resource type="cuda_compute_capability">3.0</resource>
+        <resource type="cuda_device_count_min">1</resource>
+    </requirements>
     <stdio>
         <regex match="instagraal_class" level="warning" description="instaGRAAL is raining an expected error at the end."/>
         <regex match="Exception:"/>
         <exit_code range="2:"/>
         <exit_code range=":-1"/>
     </stdio>
-    <requirements>
-        <container type="docker">koszullab/instagraal</container>
-    </requirements>
     <version_command>instagraal --version</version_command>
     <command>
     <![CDATA[
@@ -96,7 +100,6 @@
 
         <param argument="--neighborhood" type="integer" value="5" min="0" max="100" label="Number of neighbors to sample for potential mutations for each bin" />
         <param argument="--circular" type="boolean" truevalue="--circular" falsevalue="" label="Indicates genome is circular" />
-        <param argument="--bomb" type="boolean" truevalue="--bomb" falsevalue="" label="Indicates genome is circular" />
         <param argument="--bomb" type="boolean" truevalue="--bomb" falsevalue="" label="Explode the genome prior to scaffolding" />
         <param argument="--pyramid-only" type="boolean" truevalue="--pyramid-only" falsevalue="" label="Only build multi-resolution contact maps (pyramids) and don't do any scaffolding" />
         <param argument="--simple" type="boolean" truevalue="--simple" falsevalue="" label="Only perform operations at the edge of the contigs" />
@@ -104,9 +107,9 @@
 
     </inputs>
     <outputs>
-        <data name="genome" format="fasta" from_work_dir="./outputs/genome.fasta"/>
-        <data name="frags" format="tabular" from_work_dir="./outputs/info_frags.txt"/>
-        <data name="curated" format="fasta" from_work_dir="./outputs/curated.fasta"/>
+        <data name="genome" format="fasta" from_work_dir="./outputs/genome.fasta" label="${tool.name} on ${on_string}: Genome sequence"/>
+        <data name="frags" format="tabular" from_work_dir="./outputs/info_frags.txt" label="${tool.name} on ${on_string}: Fragment information"/>
+        <data name="curated" format="fasta" from_work_dir="./outputs/curated.fasta" label="${tool.name} on ${on_string}: Curated sequences"/>
     </outputs>
     <tests>
         <test>