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changeset 2:a7093d5933a8 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit de4309426401ce655435d6867b05c3673b9d086f
author nml
date Mon, 26 Mar 2018 14:23:30 -0400
parents 1abf6b32ecfd
children 8dacd75ca8f1
files aacoverage.xml callaavar.xml callcodonvar.xml callntvar.xml consensus.xml dnds.xml drmutations.xml hydra.xml
diffstat 8 files changed, 36 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/aacoverage.xml	Wed Dec 13 10:28:31 2017 -0500
+++ b/aacoverage.xml	Mon Mar 26 14:23:30 2018 -0400
@@ -1,7 +1,7 @@
 <tool id="aacoverage" name="Amino Acid Coverage" version="0.1.0">
     <description>Builds an aa census and returns its coverage</description>
     <requirements>
-          <requirement type="package" version="0.2.2">quasitools</requirement>
+          <requirement type="package" version="0.2.3">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
--- a/callaavar.xml	Wed Dec 13 10:28:31 2017 -0500
+++ b/callaavar.xml	Mon Mar 26 14:23:30 2018 -0400
@@ -1,7 +1,7 @@
 <tool id="aavariants" name="Amino Acid Variants" version="0.1.0">
     <description>Identifies amino acid mutations</description>
     <requirements>
-        <requirement type="package" version="0.2.2">quasitools</requirement>
+        <requirement type="package" version="0.2.3">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
--- a/callcodonvar.xml	Wed Dec 13 10:28:31 2017 -0500
+++ b/callcodonvar.xml	Mon Mar 26 14:23:30 2018 -0400
@@ -1,7 +1,7 @@
 <tool id="callcodonvar" name="Codon Variants" version="0.1.0">
     <description>Identifies codon variants and non-synonymous/synonymous mutations</description>
     <requirements>
-          <requirement type="package" version="0.2.2">quasitools</requirement>
+          <requirement type="package" version="0.2.3">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -53,4 +53,4 @@
     ]]></help>
     <citations>
     </citations>
-</tool>
\ No newline at end of file
+</tool>
--- a/callntvar.xml	Wed Dec 13 10:28:31 2017 -0500
+++ b/callntvar.xml	Mon Mar 26 14:23:30 2018 -0400
@@ -1,7 +1,7 @@
 <tool id="callntvar" name="Nucleotide Variants" version="0.1.0">
     <description>Identifies nucleotide variants</description>
     <requirements>
-          <requirement type="package" version="0.2.2">quasitools</requirement>
+          <requirement type="package" version="0.2.3">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
     
--- a/consensus.xml	Wed Dec 13 10:28:31 2017 -0500
+++ b/consensus.xml	Mon Mar 26 14:23:30 2018 -0400
@@ -1,15 +1,21 @@
-<tool id="consensus" name="Consensus Sequence" version="0.1.0">
+<tool id="consensus" name="Consensus Sequence" version="0.2.0">
     <description>Generate a consensus sequence from a BAM file</description>
     <requirements>
-          <requirement type="package" version="0.2.2">quasitools</requirement>
+          <requirement type="package" version="0.2.3">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
         ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
-        quasitools consensus $input_bam $ref_file  
+        quasitools consensus $input_bam $ref_file 
+
+        #if $fasta_id.type == 'default':
+            -i $input_bam.name 
+        #elif $fasta_id.type == 'custom':
+            -i $fasta_id.custom_id 
+        #end if
 
         #if $base_type.type == 'mixed':
-            -p $base_type.percentage  
+            -p $base_type.percentage 
         #end if
 
         -o output.fasta
@@ -29,6 +35,17 @@
                 <param name="percentage" type="integer" min="0" max="100" optional="true" value="100" label="Percentage" help="Percentage to include base in mixture. Defaults to 100."/>
             </when>
         </conditional>
+        <conditional name="fasta_id">
+            <param name="type" type="select" label="Specify consensus fasta identifier" multiple="false" display="radio">
+                <option value="default" >Use bam dataset name</option>
+                <option value="custom">Use custom name</option>
+            </param>
+            <when value="default">
+            </when>
+            <when value="custom">
+                <param name="custom_id" type="text" optional="false" value="custom_id" label="Fasta identifier" help="Type in a fasta identifier."/>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <data format="fasta" name="output" from_work_dir="output.fasta" />
@@ -40,7 +57,7 @@
             <param name="type" value="majority" />
             <output name="output" >
                 <assert_contents>
-                    <has_text text=">blah_100_hxb2_pol" />
+                    <has_text text=">align.bam_100_hxb2_pol" />
                     <has_text text="AGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGAT" />
                 </assert_contents>
             </output>
@@ -52,7 +69,7 @@
             <param name="percentage" value="5" />
             <output name="output" >
                 <assert_contents>
-                    <has_text text=">blah_5_hxb2_pol" />
+                    <has_text text=">align.bam_5_hxb2_pol" />
                     <has_text text="AGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAMAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGAT" />
                 </assert_contents>
             </output>
--- a/dnds.xml	Wed Dec 13 10:28:31 2017 -0500
+++ b/dnds.xml	Mon Mar 26 14:23:30 2018 -0400
@@ -1,7 +1,7 @@
 <tool id="dnds" name="dNdS Report" version="0.1.0">
     <description>Calculate the dN/dS value for each region in a bed file</description>
     <requirements>
-          <requirement type="package" version="0.2.2">quasitools</requirement>
+          <requirement type="package" version="0.2.3">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -38,4 +38,4 @@
     ]]></help>
     <citations>
     </citations>
-</tool>
\ No newline at end of file
+</tool>
--- a/drmutations.xml	Wed Dec 13 10:28:31 2017 -0500
+++ b/drmutations.xml	Mon Mar 26 14:23:30 2018 -0400
@@ -1,7 +1,7 @@
 <tool id="drmutations" name="Drug Resistance Mutations" version="0.1.0">
     <description></description>
     <requirements>
-        <requirement type="package" version="0.2.2">quasitools</requirement>
+        <requirement type="package" version="0.2.3">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
--- a/hydra.xml	Wed Dec 13 10:28:31 2017 -0500
+++ b/hydra.xml	Mon Mar 26 14:23:30 2018 -0400
@@ -1,7 +1,7 @@
 <tool id="hydra" name="Hydra pipeline" version="0.1.0">
     <description>Identifies drug resistance within an NGS dataset</description>
     <requirements>
-          <requirement type="package" version="0.2.2">quasitools</requirement>
+          <requirement type="package" version="0.2.3">quasitools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -95,7 +95,7 @@
         </conditional>
         <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Defaults to HIV mutation database." />
         <param name="reporting_threshold" type="integer" optional="true" min="1" max="100" value="1" label="Reporting threshold. Defaults to 1." help="Minimum mutation frequency to report." />
-        <param name="consensus_pct" type="integer" optional="true" min="1" max="20" value="20" label="Reporting threshold" help="Minimum mutation frequency to report. Defaults to 20." />
+        <param name="consensus_pct" type="integer" optional="true" min="1" max="20" value="20" label="Consensus percentage" help="Minimum mutation frequency to report. Defaults to 20." />
         <param name="length_cutoff" type="integer" optional="true" min="0" max="1000" label="Length cutoff" value="100" help="Reads which fall short of the specified length will be filtered out. Defaults to 100." />
         <param name="score_cutoff" type="integer" optional="true" min="0" max="40" label="Score cutoff" value="30" help="Reads whose average quality score is less than the specified score will be filtered out. Defaults to 30." />
         <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."/>
@@ -115,6 +115,9 @@
         <data format="vcf" label="HyDRA: variants output" name="output_hydra" from_work_dir="output/hydra.vcf" />
         <data format="vcf" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.hmcf" />
         <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" />
+        <data format="fasta" label="HyDRA: consensus output" name="output_consensus" from_work_dir="output/consensus.fasta">
+            <filter>generate_consensus</filter>
+        </data>
     </outputs>
     <tests>
         <test>