diff bamtools.xml @ 3:04866f817daa draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
author devteam
date Wed, 18 Jan 2017 11:47:11 -0500
parents ea3fc1adee75
children 4d343c1f606b
line wrap: on
line diff
--- a/bamtools.xml	Wed Nov 11 12:33:26 2015 -0500
+++ b/bamtools.xml	Wed Jan 18 11:47:11 2017 -0500
@@ -1,232 +1,193 @@
 <?xml version="1.0"?>
-<tool id="bamtools" name="Convert, Merge, Randomize" version="0.0.2">
-  <description>BAM datasets and perform other transformations</description>
-  <requirements>
-    <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement>
-    <requirement type="package" version="0.1.18">samtools</requirement>
-  </requirements>
-
-  <command>
-   ##set up input files
-
-  #for $bam_count, $input_bam in enumerate( $input_bams ):
-    ln -s "${input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
-    ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
-  #end for
-
-  #if str( $analysis_type.analysis_type_selector ) == "convert":
-    #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
-      #set $reference_fasta_filename = "localref.fa"
-      #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == "history":
-        ln -s "${analysis_type.format_type.reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
-        samtools faidx "${reference_fasta_filename}" 2&gt;&amp;1 || echo "Error running samtools faidx for bamtools convert" &gt;&amp;2 &amp;&amp;
-      #else:
-        #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path )
-      #end if
-    #end if
-  #end if
-
-    ##finished setting up inputs
-
-    ##start bamtools commandline
-
-    bamtools
-
-    #if str( $analysis_type.analysis_type_selector ) == "convert":
-
-    convert
-
-    -format ${analysis_type.format_type.format_type_selector}
-
-      #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
-
-      ${analysis_type.format_type.mapqual}
-      -fasta "${reference_fasta_filename}"
-
-      #elif str( $analysis_type.format_type.format_type_selector ) == "sam":
-
-      ${analysis_type.format_type.noheader}
-
-      #end if
-
-    -out $out_file1
-
-    #elif str( $analysis_type.analysis_type_selector ) == "count":
-
-    count
-    > $out_file1
-
-    #elif str( $analysis_type.analysis_type_selector ) == "coverage":
-
-    coverage
-    -out $out_file1
-
-    #elif str( $analysis_type.analysis_type_selector ) == "header":
-
-    header
-    > $out_file1
-
-    #elif str( $analysis_type.analysis_type_selector ) == "merge":
-
-    merge
-    -out $out_file1
-
-    #elif str( $analysis_type.analysis_type_selector ) == "random":
-
-    random
-    -n ${analysis_type.count}
-    -seed ${analysis_type.seed}
-    -out $out_file1
-
-    #elif str( $analysis_type.analysis_type_selector ) == "revert":
-
-    revert
-    ${analysis_type.keepDuplicate}
-    ${analysis_type.keepQualities}
-    -out $out_file1
-
-    #elif str( $analysis_type.analysis_type_selector ) == "sort":
-
-    sort
-    ${analysis_type.byname}
-    -out $out_file1
-
-    #end if
-
-    #for $bam_count, $input_bam in enumerate( $input_bams ):
-        -in "localbam_${bam_count}.bam"
-    #end for
-
-
-  </command>
-  <inputs>
-
-    <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>
-
-    <conditional name="analysis_type">
-      <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool">
-        <option value="convert">Convert</option>
-        <option value="count">Count</option>
-        <option value="coverage">Coverage</option>
-        <option value="header">Header</option>
-        <option value="merge">Merge</option>
-        <option value="random">Random</option>
-        <option value="revert">Revert</option>
-      <!-- The sort option below is commented out as BAM files in Galaxy are reference sorted by dafault. -->
-      <!-- Allowing users for sort files may break donstream functionality. -->
-      <!-- To enable sort option simply uncomment the line below: -->
-      <!--  <option value="sort">Sort</option> -->
-      </param>
-      <when value="convert">
-        <conditional name="format_type">
-          <param name="format_type_selector" type="select" help="Select what to convert your BAM to">
-           <option value="bed">BED</option>
-           <option value="fasta">FASTA</option>
-           <option value="fastq">FASTQ</option>
-           <option value="json">JSON</option>
-           <option value="pileup">Pileup</option>
-           <option value="sam">SAM</option>
-           <option value="yaml">YAML</option>
-          </param>
-          <when value="pileup">
-            <conditional name="reference_source">
-              <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-                <option value="cached">Locally cached</option>
-                <option value="history">History</option>
-              </param>
-              <when value="cached">
-                <param name="ref_file" type="select" label="Using reference genome">
-                  <options from_data_table="sam_fa_indexes">
-                  <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
-                  </options>
-                  <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
-                </param>
-              </when>
-              <when value="history"> <!-- FIX ME!!!! -->
-                <param name="ref_file" type="data" format="fasta" label="Using reference file" />
-              </when>
-            </conditional>
-            <param name="mapqual" type="boolean" truevalue="-mapqual" falsevalue="" label="Print quality scores?" />
-          </when>
-          <when value="sam">
-            <param name="noheader" type="boolean" truevalue="-noheader" falsevalue="" label="Do not print header" />
-          </when>
+<tool id="bamtools" name="Convert, Merge, Randomize" version="2.4.0">
+    <description>BAM datasets and perform other transformations</description>
+    <requirements>
+        <requirement type="package" version="2.4.0">bamtools</requirement>
+        <requirement type="package" version="1.3.1">samtools</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command>
+        <![CDATA[
+            ##set up input files
+            #for $bam_count, $input_bam in enumerate( $input_bams ):
+                ln -s "${input_bam}" "localbam_${bam_count}.bam" &&
+                ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
+            #end for
+            #if str( $analysis_type.analysis_type_selector ) == "convert":
+                #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
+                    #set $reference_fasta_filename = "localref.fa"
+                    #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == "history":
+                        ln -s "${analysis_type.format_type.reference_source.ref_file}" "${reference_fasta_filename}" &&
+                        samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for bamtools convert" >&2 &&
+                    #else:
+                        #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path )
+                    #end if
+                #end if
+            #end if
+            bamtools
+            #if str( $analysis_type.analysis_type_selector ) == "convert":
+                convert
+                -format ${analysis_type.format_type.format_type_selector}
+                #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
+                    ${analysis_type.format_type.mapqual}
+                    -fasta "${reference_fasta_filename}"
+                #elif str( $analysis_type.format_type.format_type_selector ) == "sam":
+                    ${analysis_type.format_type.noheader}
+                #end if
+                -out $out_file1
+            #elif str( $analysis_type.analysis_type_selector ) == "count":
+                count
+                > $out_file1
+            #elif str( $analysis_type.analysis_type_selector ) == "coverage":
+                coverage
+                -out $out_file1
+            #elif str( $analysis_type.analysis_type_selector ) == "header":
+                header
+                > $out_file1
+            #elif str( $analysis_type.analysis_type_selector ) == "merge":
+                merge
+                -out $out_file1
+            #elif str( $analysis_type.analysis_type_selector ) == "random":
+                random
+                -n ${analysis_type.count}
+                -seed ${analysis_type.seed}
+                -out $out_file1
+            #elif str( $analysis_type.analysis_type_selector ) == "revert":
+                revert
+                ${analysis_type.keepDuplicate}
+                ${analysis_type.keepQualities}
+                -out $out_file1
+            #elif str( $analysis_type.analysis_type_selector ) == "sort":
+                sort
+                ${analysis_type.byname}
+                -out $out_file1
+            #end if
+            #for $bam_count, $input_bam in enumerate( $input_bams ):
+                -in "localbam_${bam_count}.bam"
+            #end for
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>
+        <conditional name="analysis_type">
+            <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool">
+                <option value="convert">Convert</option>
+                <option value="count">Count</option>
+                <option value="coverage">Coverage</option>
+                <option value="header">Header</option>
+                <option value="merge">Merge</option>
+                <option value="random">Random</option>
+                <option value="revert">Revert</option>
+                <!-- The sort option below is commented out as BAM files in Galaxy are reference sorted by dafault. -->
+                <!-- Allowing users for sort files may break donstream functionality. -->
+                <!-- To enable sort option simply uncomment the line below: -->
+                <!--  <option value="sort">Sort</option> -->
+            </param>
+            <when value="convert">
+                <conditional name="format_type">
+                    <param name="format_type_selector" type="select" help="Select what to convert your BAM to">
+                        <option value="bed">BED</option>
+                        <option value="fasta">FASTA</option>
+                        <option value="fastq">FASTQ</option>
+                        <option value="json">JSON</option>
+                        <option value="pileup">Pileup</option>
+                        <option value="sam">SAM</option>
+                        <option value="yaml">YAML</option>
+                    </param>
+                    <when value="bed"/>
+                    <when value="fasta"/>
+                    <when value="fastq"/>
+                    <when value="json"/>
+                    <when value="yaml"/>
+                    <when value="pileup">
+                        <conditional name="reference_source">
+                            <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
+                                <option value="cached">Locally cached</option>
+                                <option value="history">History</option>
+                            </param>
+                            <when value="cached">
+                                <param name="ref_file" type="select" label="Using reference genome">
+                                    <options from_data_table="sam_fa_indexes">
+                                        <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
+                                    </options>
+                                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+                                </param>
+                            </when>
+                            <when value="history"> <!-- FIX ME!!!! -->
+                                <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+                            </when>
+                        </conditional>
+                        <param name="mapqual" type="boolean" truevalue="-mapqual" falsevalue="" label="Print quality scores?" />
+                    </when>
+                    <when value="sam">
+                        <param name="noheader" type="boolean" truevalue="-noheader" falsevalue="" label="Do not print header" />
+                    </when>
+                </conditional>
+            </when>
+            <when value="count" />
+            <when value="coverage" />
+            <when value="header" />
+            <when value="merge" />
+            <when value="random">
+                <param name="count" type="integer" value="10000" label="Number of random alignments to grab" help="No duplicate checking is perfomed" />
+                <param name="seed" type="integer" value="1024" label="Random number generator seed" help="Use the same seed for reproducible results" />
+            </when>
+            <when value="revert">
+                <param name="keepDuplicate" type="boolean" truevalue="-keepDuplicate" falsevalue="" label="Keep duplicates marked" help="Do not remove duplicate marks" />
+                <param name="keepQualities" type="boolean" truevalue="-keepQualities" falsevalue="" label="Keep base qualities" help="Do not replace qualities with contect of OQ tag" />
+            </when>
+            <!--
+            <when value="sort">
+                <param name="byname" type="boolean" truevalue="-byname" falsevalue="" label="Sort by name" help="Checked: sort by name; Unchecked: sort by coordinate"/>
+            </when>
+            -->
         </conditional>
-      </when>
-      <when value="count">
-      <!-- Nothing to be done with count -> just count alignments in the input bam(s) -->
-      </when>
-      <when value="coverage">
-      <!-- Nothing to be done with count -> just count alignments in the input bam(s) -->
-      </when>
-      <when value="header">
-      <!-- Nothing to be done with count -> just count alignments in the input bam(s) -->
-      </when>
-      <when value="merge">
-      <!-- Nothing to be done with count -> just count alignments in the input bam(s) -->
-      </when>
-      <when value="random">
-        <param name="count" type="integer" value="10000" label="Number of random alignments to grab" help="No duplicate checking is perfomed" />
-        <param name="seed" type="integer" value="1024" label="Random number generator seed" help="Use the same seed for reproducible results" />
-      </when>
-      <when value="revert">
-        <param name="keepDuplicate" type="boolean" truevalue="-keepDuplicate" falsevalue="" label="Keep duplicates marked" help="Do not remove duplicate marks" />
-        <param name="keepQualities" type="boolean" truevalue="-keepQualities" falsevalue="" label="Keep base qualities" help="Do not replace qualities with contect of OQ tag" />
-      </when>
-      <when value="sort">
-        <param name="byname" type="boolean" truevalue="-byname" falsevalue="" label="Sort by name" help="Checked: sort by name; Unchecked: sort by coordinate"/>
-      </when>
-    </conditional>
-
     </inputs>
     <outputs>
-      <data format="txt" name="out_file1">
-        <change_format>
-          <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" />
-          <when input="analysis_type.format_type.format_type_selector" value="fasta" format="fasta" />
-          <when input="analysis_type.format_type.format_type_selector" value="fastq" format="fastq" />
-          <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" />
-          <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" />
-          <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" />
-          <when input="analysis_type.analysis_type_selector" value="merge" format="bam" />
-          <when input="analysis_type.analysis_type_selector" value="random" format="bam" />
-          <when input="analysis_type.analysis_type_selector" value="revert" format="bam" />
-          <when input="analysis_type.analysis_type_selector" value="sort" format="bam" />
-        </change_format>
-      </data>
+        <data format="txt" name="out_file1">
+            <change_format>
+                <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" />
+                <when input="analysis_type.format_type.format_type_selector" value="fasta" format="fasta" />
+                <when input="analysis_type.format_type.format_type_selector" value="fastq" format="fastq" />
+                <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" />
+                <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" />
+                <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" />
+                <when input="analysis_type.analysis_type_selector" value="merge" format="bam" />
+                <when input="analysis_type.analysis_type_selector" value="random" format="bam" />
+                <when input="analysis_type.analysis_type_selector" value="revert" format="bam" />
+                <when input="analysis_type.analysis_type_selector" value="sort" format="bam" />
+            </change_format>
+        </data>
     </outputs>
     <tests>
-      <test>
-        <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
-        <param name="analysis_type_selector" value="convert"/>
-        <param name="format_type_selector" value="pileup"/>
-        <param name="reference_source_selector" value="history" />
-        <param name="mapqual" value="true" />
-        <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/>
-        <output name="output_bam" file="bamtools-convert-pileup.pu" />
-      </test>
-      <test>
-        <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
-        <param name="analysis_type_selector" value="count"/>
-        <output name="output_bam" file="bamtools-count.tab" />
-      </test>
-      <test>
-        <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
-        <param name="analysis_type_selector" value="coverage"/>
-        <output name="output_bam" file="bamtools-coverage.tab" />
-      </test>
-      <test>
-        <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
-        <param name="analysis_type_selector" value="header"/>
-        <output name="output_bam" file="bamtools-header.txt" />
-      </test>
+        <test>
+            <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
+            <param name="analysis_type_selector" value="convert"/>
+            <param name="format_type_selector" value="pileup"/>
+            <param name="reference_source_selector" value="history" />
+            <param name="mapqual" value="true" />
+            <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/>
+            <output name="output_bam" file="bamtools-convert-pileup.pu" />
+        </test>
+        <test>
+            <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
+            <param name="analysis_type_selector" value="count"/>
+            <output name="output_bam" file="bamtools-count.tab" />
+        </test>
+        <test>
+            <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
+            <param name="analysis_type_selector" value="coverage"/>
+            <output name="output_bam" file="bamtools-coverage.tab" />
+        </test>
+        <test>
+            <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
+            <param name="analysis_type_selector" value="header"/>
+            <output name="output_bam" file="bamtools-header.txt" />
+        </test>
     </tests>
-
-  <stdio>
-    <exit_code range="1:" />
-  </stdio>
-
-  <help>
+    <help>
 
 **What is does**
 
@@ -284,8 +245,8 @@
 
 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
 
-  </help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btr174</citation>
-  </citations>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btr174</citation>
+    </citations>
 </tool>