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changeset 7:dcd43b402eb3 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
author nml
date Fri, 23 Nov 2018 15:43:16 -0500
parents 9fb9fed71486
children 9def47f3c1e4
files aacoverage.xml callaavar.xml callcodonvar.xml callntvar.xml complexity.xml consensus.xml distance.xml dnds.xml drmutations.xml hydra.xml quality.xml
diffstat 11 files changed, 155 insertions(+), 31 deletions(-) [+]
line wrap: on
line diff
--- a/aacoverage.xml	Fri Oct 12 09:16:03 2018 -0400
+++ b/aacoverage.xml	Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
 <tool id="aacoverage" name="Amino Acid Coverage" version="0.4.2">
     <description>Builds an aa census and returns its coverage</description>
     <requirements>
-          <requirement type="package" version="0.4.2">quasitools</requirement>
+          <requirement type="package" version="0.5.1">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -45,5 +45,13 @@
 
     ]]></help>
     <citations>
+		<citation type="bibtex">
+			@misc{GitHubquasitoolsaacoverage,
+			title = {quasitools aacoverage},
+			publisher = {phac-nml},
+			journal = {GitHub repository},
+			url = {https://github.com/phac-nml/quasitools},
+			}
+		</citation>
     </citations>
 </tool>
--- a/callaavar.xml	Fri Oct 12 09:16:03 2018 -0400
+++ b/callaavar.xml	Fri Nov 23 15:43:16 2018 -0500
@@ -1,15 +1,27 @@
-<tool id="aavariants" name="Amino Acid Variants" version="0.4.2">
+<tool id="aavariants" name="Amino Acid Variants" version="0.5.1">
     <description>Identifies amino acid mutations</description>
     <requirements>
-        <requirement type="package" version="0.4.2">quasitools</requirement>
+        <requirement type="package" version="0.5.1">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
         ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
-        quasitools call aavar $input_bam $ref_file $var_file $input_genes
+		quasitools call aavar $input_bam $ref_file $input_genes 
+		
+		#if $var_file:
+			$var_file 
+		#end if
 
         #if $mutation_db:
-          $mutation_db
+        	$mutation_db
+        #end if
+
+		#if $min_freq:
+			-f $min_freq 
+		#end if
+
+		#if $error_rate:
+            -e $error_rate
         #end if
 
         -o output.vcf
@@ -18,10 +30,11 @@
     <inputs>
         <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
         <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
-        <param name="var_file" type="data" format="vcf" optional="false" label="Variants file" />
         <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
+		<param name="var_file" type="data" format="vcf" optional="true" label="Variants file" help="Not required. If not supplied, a variants file will be generated using the input bam file." />
         <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Not required. Defaults to HIV mutation database." />
         <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="The minimum required frequency. Defaults to 0.01." />
+        <param name="error_rate" type="float" optional="true" min="0" max="1" value="0.0021" label="Error rate" help="Estimated sequencing error rate. Defaults to 0.0021."/>
     </inputs>
     <outputs>
         <data format="vcf" name="output" from_work_dir="output.vcf" />
@@ -51,9 +64,19 @@
 Amino Acid Variants
 ===================
 
-Identifies amino acid mutations.
+Identifies amino acid mutations for a BAM file.
+
+
 
     ]]></help>
     <citations>
+		<citation type="bibtex">
+			@misc{GitHubquasitoolscallaavar,
+			title = {quasitools callaavar},
+			publisher = {phac-nml},
+			journal = {GitHub repository},
+			url = {https://github.com/phac-nml/quasitools},
+			}
+		</citation>
     </citations>
 </tool>
--- a/callcodonvar.xml	Fri Oct 12 09:16:03 2018 -0400
+++ b/callcodonvar.xml	Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-<tool id="callcodonvar" name="Codon Variants" version="0.4.2">
+<tool id="callcodonvar" name="Codon Variants" version="0.5.1">
     <description>Identifies codon variants and non-synonymous/synonymous mutations</description>
     <requirements>
-          <requirement type="package" version="0.4.2">quasitools</requirement>
+          <requirement type="package" version="0.5.1">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -10,6 +10,10 @@
         ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
         quasitools call codonvar $input_bam $ref_file $offset $input_genes
 
+		#if $var_file:
+			$var_file 
+		#end if
+
         #if $error_rate:
             -e $error_rate
         #end if
@@ -22,7 +26,8 @@
         <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
         <param name="offset" type="integer" optional="false" label="Offset" min="0" value="0"/>
         <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
-        <param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.01" help="Estimated sequencing error rate. Defaults to 0.01." />
+		<param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.0021" help="Estimated sequencing error rate. Defaults to 0.0021." />
+		<param name="var_file" type="data" format="vcf" optional="true" label="Variants file" help="Not required. If not supplied, a variants file will be generated using the input bam file." />
     </inputs>
     <outputs>
         <data format="csv" name="output" from_work_dir="output.csv" />
@@ -52,5 +57,13 @@
 
     ]]></help>
     <citations>
+		<citation type="bibtex">
+			@misc{GitHubquasitoolscallcodonvar,
+			title = {quasitools callcodonvar},
+			publisher = {phac-nml},
+			journal = {GitHub repository},
+			url = {https://github.com/phac-nml/quasitools},
+			}
+		</citation>
     </citations>
 </tool>
--- a/callntvar.xml	Fri Oct 12 09:16:03 2018 -0400
+++ b/callntvar.xml	Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-<tool id="callntvar" name="Nucleotide Variants" version="0.4.2">
+<tool id="callntvar" name="Nucleotide Variants" version="0.5.1">
     <description>Identifies nucleotide variants</description>
     <requirements>
-          <requirement type="package" version="0.4.2">quasitools</requirement>
+          <requirement type="package" version="0.5.1">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -18,7 +18,7 @@
     <inputs>
         <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
         <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
-        <param name="error_rate" type="float" optional="true" min="0" max="1" value="0.01" label="Error rate" help="Estimated sequencing error rate. Defaults to 0.01."/>
+        <param name="error_rate" type="float" optional="true" min="0" max="1" value="0.0021" label="Error rate" help="Estimated sequencing error rate. Defaults to 0.0021."/>
     </inputs>
     <outputs>
         <data format="vcf" name="output" from_work_dir="output.vcf" />
@@ -30,7 +30,9 @@
             <output name="output" >
                 <assert_contents>
                     <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/>
-                    <has_text_matching expression="hxb2_pol\s606\s.\sa\sc\s69\sPASS\sDP=157;AC=12;AF=0.0764" />
+                    <has_text_matching expression="hxb2_pol\s606\s.\sa\sc\s100\sPASS\sDP=157;AC=12;AF=0.0764" />
+                    <has_text_matching expression="hxb2_pol\s812\s.\sg\sa\s58\sPASS\sDP=634;AC=10;AF=0.0158" />
+                    <has_text_matching expression="hxb2_pol\s2278\s.\sc\st\s54\sPASS\sDP=557;AC=9;AF=0.0162" />
                 </assert_contents>
             </output>
         </test>
@@ -44,5 +46,13 @@
 
     ]]></help>
     <citations>
+		<citation type="bibtex">
+			@misc{GitHubquasitoolscallntvar,
+			title = {quasitools callntvar},
+			publisher = {phac-nml},
+			journal = {GitHub repository},
+			url = {https://github.com/phac-nml/quasitools},
+			}
+		</citation>
     </citations>
 </tool>
--- a/complexity.xml	Fri Oct 12 09:16:03 2018 -0400
+++ b/complexity.xml	Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-<tool id="complexity" name="Complexity" version="0.5.0">
+<tool id="complexity" name="Complexity" version="0.5.1">
     <description>measures the complexity of the quasispecies reads</description>
     <requirements>
-          <requirement type="package" version="0.5.0">quasitools</requirement>
+          <requirement type="package" version="0.5.1">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -40,5 +40,13 @@
 
 ]]></help>
     <citations>
-    </citations>
+		<citation type="bibtex">
+			@misc{GitHubquasitoolscomplexity,
+			title = {quasitools complexity},
+			publisher = {phac-nml},
+			journal = {GitHub repository},
+			url = {https://github.com/phac-nml/quasitools},
+			}
+		</citation>
+	</citations>
 </tool>
--- a/consensus.xml	Fri Oct 12 09:16:03 2018 -0400
+++ b/consensus.xml	Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-<tool id="consensus" name="Consensus Sequence" version="0.4.2">
+<tool id="consensus" name="Consensus Sequence" version="0.5.1">
     <description>Generate a consensus sequence from a BAM file</description>
     <requirements>
-          <requirement type="package" version="0.4.2">quasitools</requirement>
+          <requirement type="package" version="0.5.1">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -89,5 +89,13 @@
 
     ]]></help>
     <citations>
+		<citation type="bibtex">
+			@misc{GitHubquasitoolsconsensus,
+			title = {quasitools consensus},
+			publisher = {phac-nml},
+			journal = {GitHub repository},
+			url = {https://github.com/phac-nml/quasitools},
+			}
+		</citation>
     </citations>
 </tool>
--- a/distance.xml	Fri Oct 12 09:16:03 2018 -0400
+++ b/distance.xml	Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-<tool id="distance" name="Quasispecies Distance" version="0.4.2">
+<tool id="distance" name="Quasispecies Distance" version="0.5.1">
     <description>Calculate the evolutionary distance between viral quasispecies.</description>
     <requirements>
-          <requirement type="package" version="0.4.2">quasitools</requirement>
+          <requirement type="package" version="0.5.1">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
--- a/dnds.xml	Fri Oct 12 09:16:03 2018 -0400
+++ b/dnds.xml	Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-<tool id="dnds" name="dNdS Report" version="0.4.2">
+<tool id="dnds" name="dNdS Report" version="0.5.1">
     <description>Calculate the dN/dS value for each region in a bed file</description>
     <requirements>
-          <requirement type="package" version="0.4.2">quasitools</requirement>
+          <requirement type="package" version="0.5.1">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -37,5 +37,13 @@
 
     ]]></help>
     <citations>
+		<citation type="bibtex">
+			@misc{GitHubquasitoolsdnds,
+			title = {quasitools dnds},
+			publisher = {phac-nml},
+			journal = {GitHub repository},
+			url = {https://github.com/phac-nml/quasitools},
+			}
+		</citation>
     </citations>
 </tool>
--- a/drmutations.xml	Fri Oct 12 09:16:03 2018 -0400
+++ b/drmutations.xml	Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-<tool id="drmutations" name="Drug Resistance Mutations" version="0.4.2">
+<tool id="drmutations" name="Drug Resistance Mutations" version="0.5.1">
     <description></description>
     <requirements>
-        <requirement type="package" version="0.4.2">quasitools</requirement>
+        <requirement type="package" version="0.5.1">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -58,7 +58,37 @@
 
 Generates a report detailing the drug resistant mutations found, above the reporting threshold (default: 1%).
 
+------
+Inputs
+------
+
+1. A BAM file.
+2. A reference FASTA file.
+3. A variants (.vcf) file.
+4. A genes (.bed) file.
+5. A mutation database (.tsv) file.
+
+----------
+Parameters
+----------
+1. The minimum required frequency for a variant to be considered. Defaults to 0.01.
+2. The reporting threshold a mutation must pass to be included in the report.
+
+-------
+Outputs
+-------
+
+A CSV file containing the drug resistant mutations found.
+
     ]]></help>
-    <citations>
-    </citations>
+	<citations>
+		<citation type="bibtex">
+			@misc{GitHubquasitoolsdrmutations,
+			title = {quasitools drmutations},
+			publisher = {phac-nml},
+			journal = {GitHub repository},
+			url = {https://github.com/phac-nml/quasitools},
+			}
+			</citation>   
+	</citations>
 </tool>
--- a/hydra.xml	Fri Oct 12 09:16:03 2018 -0400
+++ b/hydra.xml	Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-<tool id="hydra" name="Hydra pipeline" version="0.4.2">
+<tool id="hydra" name="Hydra pipeline" version="0.5.1">
     <description>Identifies drug resistance within an NGS dataset</description>
     <requirements>
-          <requirement type="package" version="0.4.2">quasitools</requirement>
+          <requirement type="package" version="0.5.1">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -318,5 +318,13 @@
 
     ]]></help>
     <citations>
+		<citation type="bibtex">
+			@misc{GitHubquasitoolshydra,
+			title = {quasitools hydra},
+			publisher = {phac-nml},
+			journal = {GitHub repository},
+			url = {https://github.com/phac-nml/quasitools},
+			}
+		</citation>
     </citations>
 </tool>
--- a/quality.xml	Fri Oct 12 09:16:03 2018 -0400
+++ b/quality.xml	Fri Nov 23 15:43:16 2018 -0500
@@ -1,7 +1,7 @@
-<tool id="quality" name="Quality control" version="0.4.2">
+<tool id="quality" name="Quality control" version="0.5.1">
     <description>Performs quality control on FASTQ reads.</description>
     <requirements>
-          <requirement type="package" version="0.4.2">quasitools</requirement>
+          <requirement type="package" version="0.5.1">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -168,5 +168,13 @@
 
 Perform quality control on FASTQ reads.]]></help>
     <citations>
+		<citation type="bibtex">
+			@misc{GitHubquasitoolsquality,
+			title = {quasitools quality},
+			publisher = {phac-nml},
+			journal = {GitHub repository},
+			url = {https://github.com/phac-nml/quasitools},
+			}
+		</citation>
     </citations>
 </tool>