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changeset 44:e2b09f608636 draft

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"planemo upload for repository https://github.com/phac-nml/mob-suite commit 1904171337e41b9f714838b6f7068aefb089d11d-dirty"
author dfornika
date Thu, 14 Nov 2019 01:33:40 +0000
parents 21ccebc96bd9
children 4c5276f87370
files mob_hostrange.xml
diffstat 1 files changed, 72 insertions(+), 72 deletions(-) [+]
line wrap: on
line diff
--- a/mob_hostrange.xml	Thu Nov 14 01:19:58 2019 +0000
+++ b/mob_hostrange.xml	Thu Nov 14 01:33:40 2019 +0000
@@ -3,87 +3,87 @@
         Provides information on plasmid reproductive host range and transfer rate using both sequencing
         and experimental data from public databases (NCBI) and publications (PubMED).
     </description>
-  <requirements>
-     <requirement type="package" version="2.0.2">mob_suite</requirement>
-  </requirements>   
-  <command detect_errors="exit_code">
-  <![CDATA[
-    mob_hostrange
-      ${exact_match}
-      ${loose_match}
-      ${host_range_detailed}
-      #if str(${replicon_name}) != "":
-        --replicon_name '${replicon_name}'
-      #end if
-      #if str(${relaxase_name}) != "":
-        --relaxase_name '${relaxase_name}'
-      #end if
-      #if str(${relaxase_accession}) != "":
-        --relaxase_accession '${relaxase_accession}'
-      #end if
-      #if str(${cluster_id}) != "":
-        --cluster_id '${cluster_id}'
-      #end if
-      --inputseq "${inputseq}"
-      --outdir '.'
-  ]]>
-  </command>
-  <inputs>
-      <param name="inputseq" type="data" format="fasta" label="Input" help="plasmid FASTA file"/>
-      <param name="exact_match" type="boolean" truevalue="--exact_match" falsevalue="" checked="false"/>
-      <param name="loose_match" type="boolean" truevalue="--loose_match" falsevalue="" checked="false"/>
-      <param name="host_range_detailed" type="boolean" truevalue="--host_range_detailed" falsevalue="" checked="false"/>
-      <param name="replicon_name" type="text" />
-      <param name="relaxase_name" type="text" />
-      <param name="relaxase_accession" type="text" />
-      <param name="cluster_id" type="text" />
-  </inputs>
-  <outputs>
-    <data name="hostrange_phylostats" label="${tool.name}: Phylostats report on ${input.name}" format="tabular">
-      <discover_datasets pattern=".+hostrange_phylostats\.txt" visible="true" format="tabular" />
-    </data>
-    <data name="hostrange_report" label="${tool.name}: Hostrange report on ${input.name}" format="tabular">
-      <discover_datasets pattern=".+hostrange_report\.txt" visible="true" format="tabular" />
-    </data>
-  </outputs>
-  <tests>
-    <test>
-        <param name="inputseq" value="plasmid_476.fasta" ftype="fasta"/>
-        <assert_stderr>
-            <has_text text="RefSeq Plasmid database found no hits"/> 
-         </assert_stderr>
-    </test>
-  </tests>
-  <help>
+    <requirements>
+        <requirement type="package" version="2.0.2">mob_suite</requirement>
+    </requirements>   
+    <command detect_errors="exit_code">
+        <![CDATA[
+            mob_hostrange
+              ${exact_match}
+              ${loose_match}
+              ${host_range_detailed}
+              #if str(${replicon_name}) != '':
+                --replicon_name '${replicon_name}'
+              #end if
+              #if str(${relaxase_name}) != '':
+                --relaxase_name '${relaxase_name}'
+              #end if
+              #if str(${relaxase_accession}) != '':
+                --relaxase_accession '${relaxase_accession}'
+              #end if
+              #if str(${cluster_id}) != '':
+                --cluster_id '${cluster_id}'
+              #end if
+              --inputseq '${inputseq}'
+              --outdir '.'
+        ]]>
+    </command>
+    <inputs>
+        <param name="inputseq" type="data" format="fasta" label="Input" help="plasmid FASTA file"/>
+        <param name="exact_match" type="boolean" truevalue="--exact_match" falsevalue="" checked="false"/>
+        <param name="loose_match" type="boolean" truevalue="--loose_match" falsevalue="" checked="false"/>
+        <param name="host_range_detailed" type="boolean" truevalue="--host_range_detailed" falsevalue="" checked="false"/>
+        <param name="replicon_name" type="text" />
+        <param name="relaxase_name" type="text" />
+        <param name="relaxase_accession" type="text" />
+        <param name="cluster_id" type="text" />
+    </inputs>
+    <outputs>
+        <data name="hostrange_phylostats" label="${tool.name}: Phylostats report on ${input.name}" format="tabular">
+            <discover_datasets pattern=".+hostrange_phylostats\.txt" visible="true" format="tabular" />
+        </data>
+        <data name="hostrange_report" label="${tool.name}: Hostrange report on ${input.name}" format="tabular">
+            <discover_datasets pattern=".+hostrange_report\.txt" visible="true" format="tabular" />
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputseq" value="plasmid_476.fasta" ftype="fasta"/>
+            <assert_stderr>
+                <has_text text="RefSeq Plasmid database found no hits"/> 
+            </assert_stderr>
+        </test>
+    </tests>
+    <help>
 
-**Syntax**
+        **Syntax**
 
-This tool provides information on plasmid reproductive host range and transfer rate using both sequencing and experimental data from public databases (NCBI) and publications (PubMED). The predicted host range represents a range of putative hosts where a given plasmid can stably replicate and be maintained by the host. The host range module makes no source attribution predictions of a plasmid.
+        This tool provides information on plasmid reproductive host range and transfer rate using both sequencing and experimental data from public databases (NCBI) and publications (PubMED). The predicted host range represents a range of putative hosts where a given plasmid can stably replicate and be maintained by the host. The host range module makes no source attribution predictions of a plasmid.
 
-For more information please visit https://github.com/phac-nml/mob-suite/. 
+        For more information please visit https://github.com/phac-nml/mob-suite/. 
 
------
+        -----
 
-**Input:**
+        **Input:**
 
-A FASTA file with a single or multiple contigs (e.g. plasmid.fasta):
+        A FASTA file with a single or multiple contigs (e.g. plasmid.fasta):
 
 
-**Output:**
+        **Output:**
 
-Tab-delimited reports listing predicted hostrange information. Refer to https://github.com/phac-nml/mob-suite#mob-hostrange-report-file-format for the description of each column.
+        Tab-delimited reports listing predicted hostrange information. Refer to https://github.com/phac-nml/mob-suite#mob-hostrange-report-file-format for the description of each column.
 
 
-  </help>
-  <citations>
-    <citation type="bibtex">
-  @misc{githubmob-suite,
-  author = {Robertson J, Nash J},
-  title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
-  publisher = {GitHub},
-  journal = {GitHub repository},
-  doi = {10.1099/mgen.0.000206},
-  url = {https://github.com/phac-nml/mob-suite}
-    }</citation>
-  </citations>
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @misc{githubmob-suite,
+            author = {Robertson J, Nash J},
+            title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
+            publisher = {GitHub},
+            journal = {GitHub repository},
+            doi = {10.1099/mgen.0.000206},
+            url = {https://github.com/phac-nml/mob-suite}
+        }</citation>
+    </citations>
 </tool>