# HG changeset patch
# User iuc
# Date 1494343040 14400
# Node ID 583abf29fc8e61e1f8a15efc474edbbbc5079c3b
# Parent  bfc4517aa037d3eca6b2502cee0681c3509167f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40

diff -r bfc4517aa037 -r 583abf29fc8e macros.xml
--- a/macros.xml	Wed Nov 11 12:53:32 2015 -0500
+++ b/macros.xml	Tue May 09 11:17:20 2017 -0400
@@ -1,16 +1,17 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.2">samtools</requirement>
+            <requirement type="package" version="1.3.1">samtools</requirement>
             <yield/>
         </requirements>
     </xml>
+    <token name="@TOOL_VERSION@">1.3.1</token>
     <xml name="citations">
         <citations>
             <citation type="bibtex">
                 @misc{SAM_def,
                 title={Definition of SAM/BAM format},
-                url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
+                url = {https://samtools.github.io/hts-specs/},}
             </citation>
             <citation type="doi">10.1093/bioinformatics/btp352</citation>
             <citation type="doi">10.1093/bioinformatics/btr076</citation>
@@ -41,7 +42,7 @@
         </citations>
     </xml>
     <xml name="version_command">
-        <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
+        <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
     </xml>
     <xml name="stdio">
         <stdio>
@@ -64,7 +65,5 @@
 5. Click **Save**
 
 The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.
-
     </token>
-
 </macros>
diff -r bfc4517aa037 -r 583abf29fc8e samtools_mpileup.xml
--- a/samtools_mpileup.xml	Wed Nov 11 12:53:32 2015 -0500
+++ b/samtools_mpileup.xml	Tue May 09 11:17:20 2017 -0400
@@ -1,25 +1,30 @@
-<tool id="samtools_mpileup" name="MPileup" version="2.1.1">
-    <description>call variants</description>
+<tool id="samtools_mpileup" name="MPileup" version="2.1.3">
+    <description>multi-way pileup of variants</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
-    <command>
-    <![CDATA[
+    <command><![CDATA[
+    #for $bam_count, $input_bam in enumerate( $reference_source.input_bam ):
+        ln -s '${input_bam}' 'localbam_${bam_count}.bam' &&
+        ln -s '${input_bam.metadata.bam_index}' 'localbam_${bam_count}.bam.bai' &&
+    #end for
+
     #if $reference_source.reference_source_selector == "history":
-       ln -s "${reference_source.ref_file}" && samtools faidx `basename "${reference_source.ref_file}"` && samtools mpileup
-    #else:
-        samtools mpileup
+        ln -s '${reference_source.ref_file}' &&
+        samtools faidx `basename '${reference_source.ref_file}'` &&
     #end if
+
+    samtools mpileup
     #if $reference_source.reference_source_selector != "history":
-        -f "${reference_source.ref_file.fields.path}"
+        -f '${reference_source.ref_file.fields.path}'
     #else:
-        -f "${reference_source.ref_file}"
+        -f '${reference_source.ref_file}'
     #end if
-    #for $bam in $reference_source.input_bam:
-        "${bam}"
+    #for $bam_count, $input_bam in enumerate( $reference_source.input_bam ):
+        localbam_${bam_count}.bam
     #end for
     #if str( $advanced_options.advanced_options_selector ) == "advanced":
         #if str( $advanced_options.filter_by_flags.filter_flags ) == "filter":
@@ -31,95 +36,110 @@
             #end if
         #end if
         #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":
-            -l "$pasted_regions"
+            -l '$pasted_regions'
         #elif str( $advanced_options.limit_by_region.limit_by_regions ) == "history"
-            -l "$advanced_options.limit_by_region.bed_regions"
+            -l '$advanced_options.limit_by_region.bed_regions'
         #end if
         #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":
-            -G "$excluded_read_groups"
+            -G '$excluded_read_groups'
         #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history"
-            -G "$advanced_options.exclude_read_group.read_groups"
+            -G '$advanced_options.exclude_read_group.read_groups'
         #end if
         ${advanced_options.skip_anomalous_read_pairs}
         ${advanced_options.disable_probabilistic_realignment}
-        -C "${advanced_options.coefficient_for_downgrading}"
-        -d "${advanced_options.max_reads_per_bam}"
+        -C ${advanced_options.coefficient_for_downgrading}
+        -d ${advanced_options.max_reads_per_bam}
         ${advanced_options.extended_BAQ_computation}
-        -q "${advanced_options.minimum_mapping_quality}"
-        -Q "${advanced_options.minimum_base_quality}"
+        -q ${advanced_options.minimum_mapping_quality}
+        -Q ${advanced_options.minimum_base_quality}
         #if str( $advanced_options.region_string ):
-            -r "${advanced_options.region_string}"
+            -r '${advanced_options.region_string}'
         #end if
-
     #end if
     #if str( $genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector ) == 'perform_genotype_likelihood_computation':
-        ##
-
         ${genotype_likelihood_computation_type.output_format}
         ${genotype_likelihood_computation_type.compressed}
 
         #if str( $genotype_likelihood_computation_type.output_tags ) != "None":
-            --output-tags "${genotype_likelihood_computation_type.output_tags}"
+            --output-tags '${genotype_likelihood_computation_type.output_tags}'
         #end if
 
         #if str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'perform_indel_calling':
-            -o "${genotype_likelihood_computation_type.perform_indel_calling.gap_open_sequencing_error_probability}"
-            -e "${genotype_likelihood_computation_type.perform_indel_calling.gap_extension_sequencing_error_probability}"
-            -h "${genotype_likelihood_computation_type.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}"
-            -L "${genotype_likelihood_computation_type.perform_indel_calling.skip_indel_calling_above_sample_depth}"
-            -m "${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}"
-            --open-prob "${genotype_likelihood_computation_type.perform_indel_calling.open_seq_error_probability}"
-            -F "${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_read_fraction}"
+            --open-prob ${genotype_likelihood_computation_type.perform_indel_calling.gap_open_sequencing_error_probability}
+            -e ${genotype_likelihood_computation_type.perform_indel_calling.gap_extension_sequencing_error_probability}
+            -h ${genotype_likelihood_computation_type.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}
+            -L ${genotype_likelihood_computation_type.perform_indel_calling.skip_indel_calling_above_sample_depth}
+            -m ${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}
+            -F ${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_read_fraction}
             ${genotype_likelihood_computation_type.perform_indel_calling.gapped_read_per_sample}
             #if len( $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ):
-                -P "${ ",".join( [ str( platform.platform_entry ) for platform in $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ] ) }"
+                -P '${ ",".join( str( platform.platform_entry ) for platform in $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ) }'
             #end if
         #elif str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'do_not_perform_indel_calling':
             -I
         #end if
-
-
     #else:
         ${genotype_likelihood_computation_type.base_position_on_reads}
         ${genotype_likelihood_computation_type.output_mapping_quality}
     #end if
-    --output "$output_mpileup" 2> "$output_log"
-    ]]>
-    </command>
+    --output '$output_mpileup'
+    ]]></command>
+
+    <configfiles>
+        <configfile name="excluded_read_groups"><![CDATA[
+#set pasted_data = ''
+#if str( $advanced_options.advanced_options_selector ) == "advanced":
+    #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":
+        #set pasted_data = '\t'.join( str( $advanced_options.exclude_read_group['read_groups'] ).split() )
+    #end if
+#end if
+${pasted_data}
+        ]]></configfile>
+        <configfile name="pasted_regions"><![CDATA[
+#set pasted_data = ''
+#if str( $advanced_options.advanced_options_selector ) == "advanced":
+    #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":
+        #set pasted_data = '\t'.join( str( $advanced_options.limit_by_region['region_paste'] ).split() )
+    #end if
+#end if
+${pasted_data}
+        ]]></configfile>
+    </configfiles>
+
     <inputs>
         <conditional name="reference_source">
-            <param label="Choose the source for the reference genome" name="reference_source_selector" type="select">
+            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
                 <option value="cached">Use a built-in genome</option>
                 <option value="history">Use a genome from the history</option>
             </param>
             <when value="cached">
-                <param format="bam" label="BAM file(s)" name="input_bam" type="data" min="1" multiple="True">
+                <param name="input_bam" type="data" format="bam" multiple="True" min="1" label="BAM file(s)">
                     <validator type="unspecified_build" />
                     <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" />
                 </param>
-                <param label="Using reference genome" name="ref_file" type="select">
+                <param name="ref_file" type="select" label="Using reference genome">
                     <options from_data_table="fasta_indexes" />
                 </param>
             </when>
             <when value="history">
-                <param format="bam" label="BAM file(s)" name="input_bam" type="data" min="1" multiple="True">
+                <param name="input_bam" type="data" format="bam" multiple="True" min="1" label="BAM file(s)">
                     <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
                 </param>
-                <param format="fasta" label="Using reference genome" name="ref_file" type="data" />
+                <param name="ref_file" type="data" format="fasta" label="Using reference genome" />
             </when>
         </conditional>
         <conditional name="genotype_likelihood_computation_type">
-            <param label="Genotype Likelihood Computation" name="genotype_likelihood_computation_type_selector" type="select">
+            <param name="genotype_likelihood_computation_type_selector" type="select" label="Genotype Likelihood Computation">
                 <option selected="True" value="perform_genotype_likelihood_computation">Perform genotype likelihood computation (--VCF, --BCF options)</option>
                 <option value="do_not_perform_genotype_likelihood_computation">Do not perform genotype likelihood computation (output pileup)</option>
             </param>
             <when value="perform_genotype_likelihood_computation">
-                <param label="Choose the output format" name="output_format" type="select">
+                <param name="output_format" type="select" label="Choose the output format">
                     <option value="--VCF">VCF</option>
                     <option value="--BCF">BCF</option>
                 </param>
-                <param checked="False" falsevalue="--uncompressed" label="Compress output" name="compressed" truevalue="" type="boolean" help="--incompressed; default=False"/>
-                <param name="output_tags" optional="True" type="select" multiple="True" display="checkboxes" label="Optional tags to output" help="--output-tags">
+                <param name="compressed" argument="--uncompressed" type="boolean" truevalue="" falsevalue="--uncompressed" checked="False" label="Compress output" />
+                <param name="output_tags" argument="--output-tags" type="select" optional="True" multiple="True" display="checkboxes" label="Optional tags to output">
                     <option value="DP">DP (Number of high-quality bases)</option>
                     <option value="DPR">DRP (Number of high-quality bases for each observed allele)</option>
                     <option value="DV">DV (Number of high-quality non-reference bases)</option>
@@ -128,23 +148,22 @@
                     <option value="SP">SP (Phred-scaled strand bias P-value)</option>
                 </param>
                 <conditional name="perform_indel_calling">
-                    <param label="Perform INDEL calling" name="perform_indel_calling_selector" type="select">
+                    <param name="perform_indel_calling_selector" type="select" label="Perform INDEL calling">
                         <option selected="True" value="perform_indel_calling_def">Perform INDEL calling using default options</option>
                         <option value="perform_indel_calling">Perform INDEL calling and set advanced options</option>
-                        <option value="do_not_perform_indel_calling">Do not perform INDEL calling</option>
+                        <option value="do_not_perform_indel_calling">Do not perform INDEL calling (-I)</option>
                     </param>
                     <when value="perform_indel_calling_def" />
                     <when value="perform_indel_calling">
-                        <param label="Phred-scaled gap open sequencing error probability" name="gap_open_sequencing_error_probability" type="integer" value="40" help="--open-prob; Reducing this value leads to more indel calls; default=40"/>
-                        <param label="Phred-scaled gap extension sequencing error probability" name="gap_extension_sequencing_error_probability" type="integer" value="20" help="--ext-prob;  Reducing this value leads to longer indels. default=20"/>
-                        <param label="Coefficient for modeling homopolymer errors." name="coefficient_for_modeling_homopolymer_errors" type="integer" value="100" help="--tandem-qual; default=100"/>
-                        <param label="Skip INDEL calling if the average per-sample depth is above" name="skip_indel_calling_above_sample_depth" type="integer" value="250" help="--max-idepth; default=250"/>
-                        <param label="Minimum gapped reads for indel candidates" name="minimum_gapped_reads_for_indel_candidates" type="integer" value="1" help="--min-ireads; default=1"/>
-                        <param label="Phred-scaled gap open sequencing error probability" name="open_seq_error_probability" type="integer" value="40" help="--open-prob; Reducing this value leads to more indel calls; default=40"/>
-                        <param label="Minimum fraction of gapped reads" name="minimum_gapped_read_fraction" type="float" value="0.002" help="--gap-frac; default=0.002"/>
-                        <param checked="False" falsevalue="" label="Apply --min-ireads and --gap-frac values on a per-sample basis" name="gapped_read_per_sample" truevalue="-p" type="boolean" help="--per-sample-mF;  by default both options are applied to reads pooled from all samples"/>
-                        <repeat name="platform_list_repeat" title="Platform for INDEL candidates">
-                            <param label="Platform to use for INDEL candidates" name="platform_entry" type="text" value="" help="It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA"/>
+                        <param name="gap_open_sequencing_error_probability" argument="--open-prob" type="integer" value="40" label="Phred-scaled gap open sequencing error probability" help="Reducing this value leads to more indel calls" />
+                        <param name="gap_extension_sequencing_error_probability" argument="--ext-prob" type="integer" value="20" label="Phred-scaled gap extension sequencing error probability" help="Reducing this value leads to longer indels" />
+                        <param name="coefficient_for_modeling_homopolymer_errors" argument="--tandem-qual" type="integer" value="100" label="Coefficient for modeling homopolymer errors" />
+                        <param name="skip_indel_calling_above_sample_depth" argument="--max-idepth" type="integer" value="250" label="Skip INDEL calling if the average per-sample depth is above" />
+                        <param name="minimum_gapped_reads_for_indel_candidates" argument="--min-ireads" type="integer" value="1" label="Minimum gapped reads for indel candidates" />
+                        <param name="minimum_gapped_read_fraction" argument="--gap-frac" type="float" value="0.002" label="Minimum fraction of gapped reads" />
+                        <param name="gapped_read_per_sample" argument="--per-sample-mF" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Apply --min-ireads and --gap-frac values on a per-sample basis" help="By default both options are applied to reads pooled from all samples"/>
+                        <repeat name="platform_list_repeat" title="Platform for INDEL candidates" help="--platforms">
+                            <param name="platform_entry" type="text" value="" label="Platform to use for INDEL candidates" help="It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA"/>
                         </repeat>
                     </when>
                     <when value="do_not_perform_indel_calling" />
@@ -152,23 +171,24 @@
 
             </when>
             <when value="do_not_perform_genotype_likelihood_computation">
-                <param checked="False" falsevalue="" label="Output base positions on reads" name="base_position_on_reads" truevalue="-O" type="boolean" help="--output-BP"/>
-                <param checked="False" falsevalue="" label="Output mapping quality" name="output_mapping_quality" truevalue="-s" type="boolean" help="--output-MQ"/>
+                <param name="base_position_on_reads" argument="--output-BP" type="boolean" truevalue="-O" falsevalue="" checked="False" label="Output base positions on reads" />
+                <param name="output_mapping_quality" argument="--output-MQ" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Output mapping quality" />
             </when>
         </conditional>
         <conditional name="advanced_options">
-            <param label="Set advanced options" name="advanced_options_selector" type="select">
+            <param name="advanced_options_selector" type="select" label="Set advanced options">
                 <option selected="True" value="basic">Basic</option>
                 <option value="advanced">Advanced</option>
             </param>
+            <when value="basic" />
             <when value="advanced">
                 <conditional name="filter_by_flags">
-                    <param label="Set filter by flags" name="filter_flags" type="select">
+                    <param name="filter_flags" type="select" label="Set filter by flags">
                         <option selected="True" value="nofilter">Do not filter</option>
                         <option value="filter">Filter by flags to exclude or require</option>
                     </param>
                     <when value="filter">
-                        <param display="checkboxes" label="Require" multiple="True" name="require_flags" type="select" help="--incl-flags">
+                        <param name="require_flags" argument="--incl-flags" type="select" multiple="True" display="checkboxes" label="Require">
                             <option value="1">Read is paired</option>
                             <option value="2">Read is mapped in a proper pair</option>
                             <option value="4">The read is unmapped</option>
@@ -181,7 +201,7 @@
                             <option value="512">The read fails platform/vendor quality checks</option>
                             <option value="1024">The read is a PCR or optical duplicate</option>
                         </param>
-                        <param display="checkboxes" label="Exclude" multiple="True" name="exclude_flags" type="select" help="--excl-flags">
+                        <param name="exclude_flags" argument="--excl-flags" type="select" multiple="True" display="checkboxes" label="Exclude">
                             <option value="1">Read is paired</option>
                             <option value="2">Read is mapped in a proper pair</option>
                             <option value="4">The read is unmapped</option>
@@ -198,75 +218,72 @@
                     <when value="nofilter" />
                 </conditional>
                 <conditional name="limit_by_region">
-                    <param label="Select regions to call" name="limit_by_regions" type="select">
+                    <param name="limit_by_regions" argument="--positions" type="select" label="Select regions to call">
                         <option selected="True" value="no_limit">Do not limit</option>
-                        <option value="history">From an uploaded BED file (--positions)</option>
-                        <option value="paste">Paste a list of regions or BED (--region)</option>
+                        <option value="history">From a BED file</option>
+                        <option value="paste">Paste a list of regions or BED</option>
                     </param>
                     <when value="history">
-                        <param format="bed" label="BED file" name="bed_regions" type="data" help="--positions">
+                        <param name="bed_regions" type="data" format="bed" label="BED file">
                             <validator type="dataset_ok_validator" />
                         </param>
                     </when>
                     <when value="paste">
-                        <param area="true" help="Paste a list of regions in BED format or as a list of chromosomes and positions" label="Regions" name="region_paste" size="10x35" type="text"/>
+                        <param name="region_paste" type="text" area="true" size="10x35" label="Regions" help="Paste a list of regions in BED format or as a list of chromosomes and positions" />
                     </when>
                     <when value="no_limit" />
                 </conditional>
                 <conditional name="exclude_read_group">
-                    <param label="Select read groups to exclude" name="exclude_read_groups" type="select" help="--exclude-RG">
+                    <param name="exclude_read_groups" argument="--exclude-RG" type="select" label="Select read groups to exclude">
                         <option selected="True" value="no_limit">Do not exclude</option>
-                        <option value="history">From an uploaded text file</option>
+                        <option value="history">From a text file</option>
                         <option value="paste">Paste a list of read groups</option>
                     </param>
                     <when value="history">
-                        <param format="txt" label="Text file" name="read_groups" type="data">
+                        <param name="read_groups" type="data" format="txt" label="Text file">
                             <validator type="dataset_ok_validator" />
                         </param>
                     </when>
                     <when value="paste">
-                        <param area="true" help="Paste a list of read groups" label="Read groups" name="group_paste" size="10x35" type="text" />
+                        <param name="group_paste" type="text" area="true" size="10x35" label="Read groups" help="Paste a list of read groups" />
                     </when>
                     <when value="no_limit" />
                 </conditional>
-                <param checked="False" falsevalue="" label="Disable read-pair overlap detection" name="ignore_overlaps" truevalue="-x" type="boolean" help="--ignore-overlaps"/>
-                <param checked="False" falsevalue="" label="Do not skip anomalous read pairs in variant calling" name="skip_anomalous_read_pairs" truevalue="-A" type="boolean" help="--count-orphans"/>
-                <param checked="False" falsevalue="" label="Disable probabilistic realignment for the computation of base alignment quality (BAQ)" name="disable_probabilistic_realignment" truevalue="-B" type="boolean" help="--no-BAQ; BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments"/>
-                <param label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" name="coefficient_for_downgrading" type="integer" value="0" help="--adjust-MQ; Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50. default=0"/>
-                <param label="Max reads per BAM" max="1024" min="1" name="max_reads_per_bam" type="integer" value="250" help="--max-depth; default=250"/>
-                <param checked="False" falsevalue="" label="Redo BAQ computation" name="extended_BAQ_computation" truevalue="-E" type="boolean" help="--redo-BAQ; ignore existing BQ tags"/>
-                <param label="Minimum mapping quality for an alignment to be used" name="minimum_mapping_quality" type="integer" value="0" help="-min-MQ; default=0"/>
-                <param label="Minimum base quality for a base to be considered" name="minimum_base_quality" type="integer" value="13" help="--min-BQ; default=13"/>
-                <param label="Only generate pileup in region" name="region_string" type="text" value="" help="--region; If used in conjunction with --positions, then considers the intersection of the two requests. Defaults to all sites" />
+                <param name="ignore_overlaps" argument="--ignore-overlaps" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Disable read-pair overlap detection" />
+                <param name="skip_anomalous_read_pairs" argument="--count-orphans" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" />
+                <param name="disable_probabilistic_realignment" argument="--no-BAQ" type="boolean" truevalue="-B" falsevalue="" checked="False" label="Disable probabilistic realignment for the computation of base alignment quality (BAQ)" help="BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments" />
+                <param name="coefficient_for_downgrading" argument="--adjust-MQ" type="integer" value="0" label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" help="Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50" />
+                <param name="max_reads_per_bam" argument="--max-depth" type="integer" max="1024" min="1" value="250" label="Max reads per BAM" />
+                <param name="extended_BAQ_computation" argument="--redo-BAQ" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Redo BAQ computation" help="Ignore existing BQ tags" />
+                <param name="minimum_mapping_quality" argument="--min-MQ" type="integer" value="0" label="Minimum mapping quality for an alignment to be used" />
+                <param name="minimum_base_quality" argument="--min-BQ" type="integer" value="13" label="Minimum base quality for a base to be considered" />
+                <param name="region_string" argument="--region" type="text" value="" label="Only generate pileup in region" help="If used in conjunction with --positions, then considers the intersection of the two requests. Defaults to all sites" />
             </when>
-            <when value="basic" />
         </conditional>
     </inputs>
     <outputs>
-        <data format="pileup" label="${tool.name} on ${on_string}" name="output_mpileup">
+        <data name="output_mpileup" format="pileup" label="${tool.name} on ${on_string}">
             <change_format>
                 <when format="bcf" input="genotype_likelihood_computation_type.output_format" value="--BCF" />
                 <when format="vcf" input="genotype_likelihood_computation_type.output_format" value="--VCF" />
             </change_format>
         </data>
-        <data format="txt" label="${tool.name} on ${on_string} (log)" name="output_log" />
     </outputs>
     <tests>
         <test>
             <param name="reference_source_selector" value="history" />
-            <param ftype="fasta" name="ref_file" value="phiX.fasta" />
-            <param ftype="bam" name="input_bam" value="samtools_mpileup_in_1.bam" />
+            <param name="ref_file" ftype="fasta" value="phiX.fasta" />
+            <param name="input_bam" ftype="bam" value="samtools_mpileup_in_1.bam" />
             <param name="genotype_likelihood_computation_type_selector" value="do_not_perform_genotype_likelihood_computation" />
             <param name="advanced_options_selector" value="basic" />
             <param name="base_position_on_reads" value="true" />
             <param name="output_mapping_quality" value="true" />
-            <output file="samtools_mpileup_out_1.pileup" name="output_mpileup" />
-            <output file="samtools_mpileup_out_1.log" name="output_log" />
+            <output name="output_mpileup" file="samtools_mpileup_out_1.pileup" />
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
-            <param ftype="fasta" name="ref_file" value="phiX.fasta" />
-            <param ftype="bam" name="input_bam" value="phiX.bam" />
+            <param name="ref_file" ftype="fasta" value="phiX.fasta" />
+            <param name="input_bam" ftype="bam" value="phiX.bam" />
             <param name="genotype_likelihood_computation_type_selector" value="perform_genotype_likelihood_computation" />
             <param name="gap_extension_sequencing_error_probability" value="20" />
             <param name="coefficient_for_modeling_homopolymer_errors" value="100" />
@@ -276,93 +293,27 @@
             <param name="platform_list_repeat" value="0" />
             <param name="advanced_options_selector" value="basic" />
             <param name="genotype_likelihood_computation_type|output_format" value="VCF" />
-            <output file="samtools_mpileup_out_2.vcf" ftype="vcf" lines_diff="8" name="output_mpileup" />
-            <output file="samtools_mpileup_out_2.log" name="output_log" />
+            <output name="output_mpileup" file="samtools_mpileup_out_2.vcf" ftype="vcf" lines_diff="8" />
+        </test>
+        <test>
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_file" ftype="fasta" value="phiX.fasta" />
+            <param name="input_bam" ftype="bam" value="samtools_mpileup_in_1.bam" />
+            <param name="genotype_likelihood_computation_type_selector" value="do_not_perform_genotype_likelihood_computation" />
+            <param name="advanced_options_selector" value="advanced" />
+            <param name="minimum_base_quality" value="0" /><!-- most reads have ultra low quality resuling in empty columns -->
+            <param name="base_position_on_reads" value="true" />
+            <param name="output_mapping_quality" value="true" />
+            <output name="output_mpileup" file="samtools_mpileup_out_3.pileup" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
-Report variants for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample.
-
-------
-
-**Input options**::
-
-  -6, --illumina1.3+      quality is in the Illumina-1.3+ encoding
-  -A, --count-orphans     do not discard anomalous read pairs
-  -b, --bam-list FILE     list of input BAM filenames, one per line
-  -B, --no-BAQ            disable BAQ (per-Base Alignment Quality)
-  -C, --adjust-MQ INT     adjust mapping quality; recommended:50, disable:0 [0]
-  -d, --max-depth INT     max per-BAM depth; avoids excessive memory usage [250]
-  -E, --redo-BAQ          recalculate BAQ on the fly, ignore existing BQs
-  -f, --fasta-ref FILE    faidx indexed reference sequence file
-  -G, --exclude-RG FILE   exclude read groups listed in FILE
-  -l, --positions FILE    skip unlisted positions (chr pos) or regions (BED)
-  -q, --min-MQ INT        skip alignments with mapQ smaller than INT [0]
-  -Q, --min-BQ INT        skip bases with baseQ/BAQ smaller than INT [13]
-  -r, --region REG        region in which pileup is generated
-  -R, --ignore-RG         ignore RG tags (one BAM = one sample)
-  --rf, --incl-flags STR|INT  required flags: skip reads with mask bits unset []
-  --ff, --excl-flags STR|INT  filter flags: skip reads with mask bits set
-                                            [UNMAP,SECONDARY,QCFAIL,DUP]
-  -x, --ignore-overlaps   disable read-pair overlap detection
-
-**Output options**::
-
-  -o, --output FILE       write output to FILE [standard output]
-  -g, --BCF               generate genotype likelihoods in BCF format
-  -v, --VCF               generate genotype likelihoods in VCF format
-
-**Output options for mpileup format** (without -g/-v)::
-
-  -O, --output-BP         output base positions on reads
-  -s, --output-MQ         output mapping quality
-
-**Output options for genotype likelihoods** (when -g/-v is used)::
-
-  -t, --output-tags LIST  optional tags to output: DP,DPR,DV,DP4,INFO/DPR,SP []
-  -u, --uncompressed      generate uncompressed VCF/BCF output
-
-**SNP/INDEL genotype likelihoods options** (effective with -g/-v)::
-
-  -e, --ext-prob INT      Phred-scaled gap extension seq error probability [20]
-  -F, --gap-frac FLOAT    minimum fraction of gapped reads [0.002]
-  -h, --tandem-qual INT   coefficient for homopolymer errors [100]
-  -I, --skip-indels       do not perform indel calling
-  -L, --max-idepth INT    maximum per-sample depth for INDEL calling [250]
-  -m, --min-ireads INT    minimum number gapped reads for indel candidates [1]
-  -o, --open-prob INT     Phred-scaled gap open seq error probability [40]
-  -p, --per-sample-mF     apply -m and -F per-sample for increased sensitivity
-  -P, --platforms STR     comma separated list of platforms for indels [all]
+Report variants for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines.
+If sample identifiers are absent, each input file is regarded as one sample.
 
 **Notes**: Assuming diploid individuals.
-]]>
-    </help>
-    <configfiles>
-        <configfile name="excluded_read_groups">
-<![CDATA[
-#set pasted_data = ''
-#if str( $advanced_options.advanced_options_selector ) == "advanced":
-    #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":
-        #set pasted_data = '\t'.join( str( $advanced_options.exclude_read_group['read_groups'] ).split() )
-    #end if
-#end if
-${pasted_data}
-]]>
-        </configfile>
-        <configfile name="pasted_regions">
-<![CDATA[
-#set pasted_data = ''
-#if str( $advanced_options.advanced_options_selector ) == "advanced":
-    #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":
-        #set pasted_data = '\t'.join( str( $advanced_options.limit_by_region['region_paste'] ).split() )
-    #end if
-#end if
-${pasted_data}
-]]>
-        </configfile>
-    </configfiles>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools/mpileup/samtools_mpileup_out_1.log
--- a/test-data/samtools/mpileup/samtools_mpileup_out_1.log	Wed Nov 11 12:53:32 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools/mpileup/samtools_mpileup_out_1.pileup
--- a/test-data/samtools/mpileup/samtools_mpileup_out_1.pileup	Wed Nov 11 12:53:32 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-phiX174	1411	A	1	^P.	$
-phiX174	1412	G	3	.^D.^F.	"$$
-phiX174	1413	C	5	...^D.^F.	"""$$
-phiX174	1414	G	6	.....^F.	#####$
-phiX174	1415	C	7	......^F.	%%%%%%&
-phiX174	1416	C	8	.......^F.	$$$$$$$$
-phiX174	1417	G	9	........^F.	"#######$
-phiX174	1418	T	10	.........^F.	"""""""""$
-phiX174	1419	G	10	..........	"""""'&'%$
-phiX174	1420	G	10	..........	""""""""""
-phiX174	1421	A	10	..........	""""""""""
-phiX174	1422	T	10	..........	""""""""""
-phiX174	1423	G	10	..........	"""""""""#
-phiX174	1424	C	10	..A.AAAAAA	%"""""""""
-phiX174	1425	C	10	..........	$$$"""""""
-phiX174	1426	T	10	..........	#####"""""
-phiX174	1427	G	10	..........	######""""
-phiX174	1428	A	10	..........	""""""""""
-phiX174	1429	C	10	..........	((((((&(""
-phiX174	1430	C	10	..........	$$$$$$$$$"
-phiX174	1431	G	10	..........	##########
-phiX174	1432	T	10	..........	""""""""""
-phiX174	1433	A	10	..........	##########
-phiX174	1434	C	10	..........	((((((&(%$
-phiX174	1435	C	10	..........	$$$$$$$$$$
-phiX174	1436	G	10	..........	##########
-phiX174	1437	A	10	..........	"""""""""!
-phiX174	1438	G	10	..........	"""""####!
-phiX174	1439	G	10	..........	"""""""""!
-phiX174	1440	C	10	..........	"""""""""!
-phiX174	1441	T	10	..........	""""""""#!
-phiX174	1442	A	10	..........	$$$%%%&&%!
-phiX174	1443	A	10	.-1C.-1C..-1C......	"""""""""!
-phiX174	1444	C	10	**.*......	&%"!"""""!
-phiX174	1445	C	10	..........	&%&!%%%&%!
-phiX174	1446	C	10	..........	"""!"""""!
-phiX174	1447	T	10	.$..$.......	#"#!"""""!
-phiX174	1448	A	8	.$..$.....	#!#%%$$!
-phiX174	1449	A	6	.$.$....	!""""!
-phiX174	1450	T	4	.$...	"""!
-phiX174	1451	G	3	.$..	#"!
-phiX174	1452	A	2	.$.	"!
-phiX174	1453	G	1	.$	!
diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools/mpileup/samtools_mpileup_out_2.bcf
Binary file test-data/samtools/mpileup/samtools_mpileup_out_2.bcf has changed
diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools_mpileup_out_1.log
--- a/test-data/samtools_mpileup_out_1.log	Wed Nov 11 12:53:32 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-[fai_load] build FASTA index.
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools_mpileup_out_1.pileup
--- a/test-data/samtools_mpileup_out_1.pileup	Wed Nov 11 12:53:32 2015 -0500
+++ b/test-data/samtools_mpileup_out_1.pileup	Tue May 09 11:17:20 2017 -0400
@@ -1,43 +1,43 @@
-phiX174	1411	A	0				1
-phiX174	1412	G	0				2,1,1
-phiX174	1413	C	0				3,2,2,1,1
-phiX174	1414	G	0				4,3,3,2,2,1
-phiX174	1415	C	0				5,4,4,3,3,2,1
-phiX174	1416	C	0				6,5,5,4,4,3,2,1
-phiX174	1417	G	0				7,6,6,5,5,4,3,2,1
-phiX174	1418	T	0				8,7,7,6,6,5,4,3,2,1
-phiX174	1419	G	0				9,8,8,7,7,6,5,4,3,2
-phiX174	1420	G	0				10,9,9,8,8,7,6,5,4,3
-phiX174	1421	A	0				11,10,10,9,9,8,7,6,5,4
-phiX174	1422	T	0				12,11,11,10,10,9,8,7,6,5
-phiX174	1423	G	0				13,12,12,11,11,10,9,8,7,6
-phiX174	1424	C	0				14,13,13,12,12,11,10,9,8,7
-phiX174	1425	C	0				15,14,14,13,13,12,11,10,9,8
-phiX174	1426	T	0				16,15,15,14,14,13,12,11,10,9
-phiX174	1427	G	0				17,16,16,15,15,14,13,12,11,10
-phiX174	1428	A	0				18,17,17,16,16,15,14,13,12,11
-phiX174	1429	C	0				19,18,18,17,17,16,15,14,13,12
-phiX174	1430	C	0				20,19,19,18,18,17,16,15,14,13
-phiX174	1431	G	0				21,20,20,19,19,18,17,16,15,14
-phiX174	1432	T	0				22,21,21,20,20,19,18,17,16,15
-phiX174	1433	A	0				23,22,22,21,21,20,19,18,17,16
-phiX174	1434	C	0				24,23,23,22,22,21,20,19,18,17
-phiX174	1435	C	0				25,24,24,23,23,22,21,20,19,18
-phiX174	1436	G	0				26,25,25,24,24,23,22,21,20,19
-phiX174	1437	A	0				27,26,26,25,25,24,23,22,21,20
-phiX174	1438	G	0				28,27,27,26,26,25,24,23,22,21
-phiX174	1439	G	0				29,28,28,27,27,26,25,24,23,22
-phiX174	1440	C	0				30,29,29,28,28,27,26,25,24,23
-phiX174	1441	T	0				31,30,30,29,29,28,27,26,25,24
-phiX174	1442	A	0				32,31,31,30,30,29,28,27,26,25
-phiX174	1443	A	0				33,32,32,31,31,30,29,28,27,26
-phiX174	1444	C	0				34,33,33,32,32,31,30,29,28,27
-phiX174	1445	C	0				34,33,34,32,33,32,31,30,29,28
-phiX174	1446	C	0				35,34,35,33,34,33,32,31,30,29
-phiX174	1447	T	0				36,35,36,34,35,34,33,32,31,30
-phiX174	1448	A	0				36,35,36,35,34,33,32,31
-phiX174	1449	A	0				36,36,35,34,33,32
-phiX174	1450	T	0				36,35,34,33
-phiX174	1451	G	0				36,35,34
-phiX174	1452	A	0				36,35
-phiX174	1453	G	0				36
+phiX174	1411	A	0				
+phiX174	1412	G	0				
+phiX174	1413	C	0				
+phiX174	1414	G	0				
+phiX174	1415	C	0				
+phiX174	1416	C	0				
+phiX174	1417	G	0				
+phiX174	1418	T	0				
+phiX174	1419	G	0				
+phiX174	1420	G	0				
+phiX174	1421	A	0				
+phiX174	1422	T	0				
+phiX174	1423	G	0				
+phiX174	1424	C	0				
+phiX174	1425	C	0				
+phiX174	1426	T	0				
+phiX174	1427	G	0				
+phiX174	1428	A	0				
+phiX174	1429	C	0				
+phiX174	1430	C	0				
+phiX174	1431	G	0				
+phiX174	1432	T	0				
+phiX174	1433	A	0				
+phiX174	1434	C	0				
+phiX174	1435	C	0				
+phiX174	1436	G	0				
+phiX174	1437	A	0				
+phiX174	1438	G	0				
+phiX174	1439	G	0				
+phiX174	1440	C	0				
+phiX174	1441	T	0				
+phiX174	1442	A	0				
+phiX174	1443	A	0				
+phiX174	1444	C	0				
+phiX174	1445	C	0				
+phiX174	1446	C	0				
+phiX174	1447	T	0				
+phiX174	1448	A	0				
+phiX174	1449	A	0				
+phiX174	1450	T	0				
+phiX174	1451	G	0				
+phiX174	1452	A	0				
+phiX174	1453	G	0				
diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools_mpileup_out_2.log
--- a/test-data/samtools_mpileup_out_2.log	Wed Nov 11 12:53:32 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-[fai_load] build FASTA index.
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools_mpileup_out_2.vcf
--- a/test-data/samtools_mpileup_out_2.vcf	Wed Nov 11 12:53:32 2015 -0500
+++ b/test-data/samtools_mpileup_out_2.vcf	Tue May 09 11:17:20 2017 -0400
@@ -4,7 +4,7 @@
 ##samtoolsCommand=samtools mpileup --VCF --uncompressed -f /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_735.dat -g -e 20 -h 100 -L 250 -m 1 --open-prob 40 -F 0.002 -e 40 --output /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_736.dat /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_734.dat
 ##reference=file:///tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_735.dat
 ##contig=<ID=phiX174,length=5386>
-##ALT=<ID=X,Description="Represents allele(s) other than observed.">
+##ALT=<ID=*,Description="Represents allele(s) other than observed.">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
 ##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
@@ -19,4 +19,4 @@
 ##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
 ##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	/tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_734.dat
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	localbam_0.bam
diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools_mpileup_out_3.log
--- a/test-data/samtools_mpileup_out_3.log	Wed Nov 11 12:53:32 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools_mpileup_out_3.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_mpileup_out_3.pileup	Tue May 09 11:17:20 2017 -0400
@@ -0,0 +1,43 @@
+phiX174	1411	A	1	^P.	$	P	1
+phiX174	1412	G	3	.^D.^F.	"$$	PDF	2,1,1
+phiX174	1413	C	5	...^D.^F.	"""$$	PDFDF	3,2,2,1,1
+phiX174	1414	G	6	.....^F.	#####$	PDFDFF	4,3,3,2,2,1
+phiX174	1415	C	7	......^F.	%%%%%%&	PDFDFFF	5,4,4,3,3,2,1
+phiX174	1416	C	8	.......^F.	$$$$$$$$	PDFDFFFF	6,5,5,4,4,3,2,1
+phiX174	1417	G	9	........^F.	"#######$	PDFDFFFFF	7,6,6,5,5,4,3,2,1
+phiX174	1418	T	10	.........^F.	"""""""""$	PDFDFFFFFF	8,7,7,6,6,5,4,3,2,1
+phiX174	1419	G	10	..........	"""""'&'%$	PDFDFFFFFF	9,8,8,7,7,6,5,4,3,2
+phiX174	1420	G	10	..........	""""""""""	PDFDFFFFFF	10,9,9,8,8,7,6,5,4,3
+phiX174	1421	A	10	..........	""""""""""	PDFDFFFFFF	11,10,10,9,9,8,7,6,5,4
+phiX174	1422	T	10	..........	""""""""""	PDFDFFFFFF	12,11,11,10,10,9,8,7,6,5
+phiX174	1423	G	10	..........	"""""""""#	PDFDFFFFFF	13,12,12,11,11,10,9,8,7,6
+phiX174	1424	C	10	..A.AAAAAA	%"""""""""	PDFDFFFFFF	14,13,13,12,12,11,10,9,8,7
+phiX174	1425	C	10	..........	$$$"""""""	PDFDFFFFFF	15,14,14,13,13,12,11,10,9,8
+phiX174	1426	T	10	..........	#####"""""	PDFDFFFFFF	16,15,15,14,14,13,12,11,10,9
+phiX174	1427	G	10	..........	######""""	PDFDFFFFFF	17,16,16,15,15,14,13,12,11,10
+phiX174	1428	A	10	..........	""""""""""	PDFDFFFFFF	18,17,17,16,16,15,14,13,12,11
+phiX174	1429	C	10	..........	((((((&(""	PDFDFFFFFF	19,18,18,17,17,16,15,14,13,12
+phiX174	1430	C	10	..........	$$$$$$$$$"	PDFDFFFFFF	20,19,19,18,18,17,16,15,14,13
+phiX174	1431	G	10	..........	##########	PDFDFFFFFF	21,20,20,19,19,18,17,16,15,14
+phiX174	1432	T	10	..........	""""""""""	PDFDFFFFFF	22,21,21,20,20,19,18,17,16,15
+phiX174	1433	A	10	..........	##########	PDFDFFFFFF	23,22,22,21,21,20,19,18,17,16
+phiX174	1434	C	10	..........	((((((&(%$	PDFDFFFFFF	24,23,23,22,22,21,20,19,18,17
+phiX174	1435	C	10	..........	$$$$$$$$$$	PDFDFFFFFF	25,24,24,23,23,22,21,20,19,18
+phiX174	1436	G	10	..........	##########	PDFDFFFFFF	26,25,25,24,24,23,22,21,20,19
+phiX174	1437	A	10	..........	"""""""""!	PDFDFFFFFF	27,26,26,25,25,24,23,22,21,20
+phiX174	1438	G	10	..........	"""""####!	PDFDFFFFFF	28,27,27,26,26,25,24,23,22,21
+phiX174	1439	G	10	..........	"""""""""!	PDFDFFFFFF	29,28,28,27,27,26,25,24,23,22
+phiX174	1440	C	10	..........	"""""""""!	PDFDFFFFFF	30,29,29,28,28,27,26,25,24,23
+phiX174	1441	T	10	..........	""""""""#!	PDFDFFFFFF	31,30,30,29,29,28,27,26,25,24
+phiX174	1442	A	10	..........	$$$%%%&&%!	PDFDFFFFFF	32,31,31,30,30,29,28,27,26,25
+phiX174	1443	A	10	.-1C.-1C..-1C......	"""""""""!	PDFDFFFFFF	33,32,32,31,31,30,29,28,27,26
+phiX174	1444	C	10	**.*......	!!"!"""""!	PDFDFFFFFF	34,33,33,32,32,31,30,29,28,27
+phiX174	1445	C	10	..........	!!&!%%%&%!	PDFDFFFFFF	34,33,34,32,33,32,31,30,29,28
+phiX174	1446	C	10	..........	!!"!"""""!	PDFDFFFFFF	35,34,35,33,34,33,32,31,30,29
+phiX174	1447	T	10	.$..$.......	!!#!"""""!	PDFDFFFFFF	36,35,36,34,35,34,33,32,31,30
+phiX174	1448	A	8	.$..$.....	!!#%%$$!	DDFFFFFF	36,35,36,35,34,33,32,31
+phiX174	1449	A	6	.$.$....	!""""!	DFFFFF	36,36,35,34,33,32
+phiX174	1450	T	4	.$...	"""!	FFFF	36,35,34,33
+phiX174	1451	G	3	.$..	#"!	FFF	36,35,34
+phiX174	1452	A	2	.$.	"!	FF	36,35
+phiX174	1453	G	1	.$	!	F	36
diff -r bfc4517aa037 -r 583abf29fc8e test-data/samtools_mpileup_out_4.log
--- a/test-data/samtools_mpileup_out_4.log	Wed Nov 11 12:53:32 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
diff -r bfc4517aa037 -r 583abf29fc8e tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Nov 11 12:53:32 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="samtools" version="1.2">
-        <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>