--- a/samtools_stats.xml	Wed Nov 11 12:55:15 2015 -0500
+++ b/samtools_stats.xml	Tue May 09 11:19:01 2017 -0400
@@ -1,144 +1,171 @@
-<tool id="samtools_stats" name="Stats" version="2.0">
+<tool id="samtools_stats" name="Stats" version="2.0.1">
     <description>generate statistics for BAM dataset</description>
     <macros>
-    <import>macros.xml</import>
-  </macros>
-    <expand macro="requirements"></expand>
-    <expand macro="stdio"></expand>
-    <expand macro="version_command"></expand>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
     <command><![CDATA[
         #if $use_reference.use_ref_selector == "yes":
             #if $use_reference.reference_source.reference_source_selector == "history":
-               ln -s "${use_reference.reference_source.ref_file}" && samtools faidx `basename "${use_reference.reference_source.ref_file}"` && samtools stats
-            #else:
-                samtools stats
-            #end if
-        #else:
-            samtools stats
-        #end if
-        "${input_file}"
-        --coverage ${coverage_min},${coverage_max},${coverage_step}
-        ${remove_dups}
-        #if str( $filter_by_flags.filter_flags ) == "filter":
-            #if $filter_by_flags.require_flags:
-                --required-flag ${sum([int(flag) for flag in str($filter_by_flags.require_flags).split(',')])}
-            #end if
-            #if $filter_by_flags.exclude_flags:
-                --filtering-flag ${sum([int(flag) for flag in str($filter_by_flags.exclude_flags).split(',')])}
+               ln -s '${use_reference.reference_source.ref_file}' &&
+               samtools faidx `basename '${use_reference.reference_source.ref_file}'` &&
             #end if
         #end if
-        --GC-depth ${gc_depth}
-        --insert-size ${insert_size}
+
+        samtools stats
+            '${input_file}'
+            --coverage ${coverage_min},${coverage_max},${coverage_step}
+            ${remove_dups}
 
-        ## The code below is commented out because using -I/--id options causes the following exception
-        ## Samtools-htslib: init_group_id() header parsing not yet implemented
+            #if str( $filter_by_flags.filter_flags ) == "filter":
+                #if $filter_by_flags.require_flags:
+                    --required-flag ${sum([int(flag) for flag in str($filter_by_flags.require_flags).split(',')])}
+                #end if
+                #if $filter_by_flags.exclude_flags:
+                    --filtering-flag ${sum([int(flag) for flag in str($filter_by_flags.exclude_flags).split(',')])}
+                #end if
+            #end if
 
-        ##if str($read_group) != "":
-        ##    -I "${read_group}"
-        ##end if
+            --GC-depth ${gc_depth}
+            --insert-size ${insert_size}
 
-        #if str($read_length) != "0":
-            --read-length "${read_length}"
-        #end if
-        --most-inserts ${most_inserts}
-        --trim-quality ${trim_quality}
-        #if $use_reference.use_ref_selector == "yes":
-            #if $use_reference.reference_source.reference_source_selector != "history":
-                --ref-seq "${use_reference.reference_source.ref_file.fields.path}"
-            #else:
-                --ref-seq "${use_reference.reference_source.ref_file}"
+            ## The code below is commented out because using -I/--id options causes the following exception
+            ## Samtools-htslib: init_group_id() header parsing not yet implemented
+            ##if str($read_group) != "":
+            ##    -I "${read_group}"
+            ##end if
+
+            #if str($read_length):
+                --read-length ${read_length}
             #end if
-        #end if
-        > "${output}"
+
+            --most-inserts ${most_inserts}
+            --trim-quality ${trim_quality}
+
+            #if $use_reference.use_ref_selector == "yes":
+                #if $use_reference.reference_source.reference_source_selector != "history":
+                    --ref-seq '${use_reference.reference_source.ref_file.fields.path}'
+                #else:
+                    --ref-seq '${use_reference.reference_source.ref_file}'
+                #end if
+            #end if
+            > '${output}'
+
         #if $split_output.split_output_selector == "yes":
             #set outputs_to_split = str($split_output.generate_tables).split(',')
-            && mkdir split && echo ${split_output.generate_tables} &&
+            && mkdir split &&
+            echo ${split_output.generate_tables}
 
             #if 'sn' in $outputs_to_split:
-                echo "# Summary Numbers\n"  > "split/Summary numbers.tab" &&
-                grep -q ^SN  "${output}" ; if [ $? = 0 ] ; then grep ^SN  "${output}" | cut -f 2- >> "split/Summary numbers.tab"  ; fi &&
+                && echo "# Summary Numbers" > 'split/Summary numbers.tab' &&
+                echo "" >> 'split/Summary numbers.tab' &&
+                if grep -q ^SN '${output}'; then
+                    grep ^SN '${output}' | cut -f 2- >> 'split/Summary numbers.tab';
+                fi
             #end if
 
             #if 'ffq' in $outputs_to_split:
-                echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > "split/First Fragment Qualities.tab" &&
-                grep -q ^FFQ "${output}" ; if [ $? = 0 ] ; then grep ^FFQ "${output}" | cut -f 2- >> "split/First Fragment Qualities.tab" ; fi &&
+                && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > 'split/First Fragment Qualities.tab' &&
+                if grep -q ^FFQ '${output}'; then
+                    grep ^FFQ '${output}' | cut -f 2- >> 'split/First Fragment Qualities.tab';
+                fi
             #end if
 
             #if 'lfq' in $outputs_to_split:
-                echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > "split/Last Fragment Qualities.tab" &&
-                grep -q ^LFQ "${output}" ; if [ $? = 0 ] ; then grep ^LFQ "${output}" | cut -f 2- >> "split/Last Fragment Qualities.tab" ; fi &&
+                && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > 'split/Last Fragment Qualities.tab' &&
+                if grep -q ^LFQ '${output}'; then
+                    grep ^LFQ '${output}' | cut -f 2- >> 'split/Last Fragment Qualities.tab';
+                fi
             #end if
 
             #if 'mpc' in $outputs_to_split:
-                echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > "split/Mismatches per cycle.tab" &&
-                grep -q ^MPC "${output}" ; if [ $? = 0 ] ; then grep ^MPC "${output}" | cut -f 2- >> "split/Mismatches per cycle.tab" ; fi &&
+                && echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > 'split/Mismatches per cycle.tab' &&
+                if grep -q ^MPC '${output}'; then
+                    grep ^MPC '${output}' | cut -f 2- >> 'split/Mismatches per cycle.tab';
+                fi
             #end if
 
             #if 'gcf' in $outputs_to_split:
-                echo "# GC Content of first fragments" > "split/GC Content of first fragments.tab" &&
-                grep -q ^GCF "${output}" ; if [ $? = 0 ] ; then grep ^GCF "${output}" | cut -f 2- >> "split/GC Content of first fragments.tab" ; fi &&
+                && echo "# GC Content of first fragments" > 'split/GC Content of first fragments.tab' &&
+                if grep -q ^GCF '${output}'; then
+                    grep ^GCF '${output}' | cut -f 2- >> 'split/GC Content of first fragments.tab';
+                fi
             #end if
 
             #if 'gcl' in $outputs_to_split:
-                echo "# GC Content of last fragments" > "split/GC Content of last fragments.tab" &&
-                grep -q ^GCL "${output}" ; if [ $? = 0 ] ; then grep ^GCL "${output}" | cut -f 2- >> "split/GC Content of last fragments.tab" ; fi &&
+                && echo "# GC Content of last fragments" > 'split/GC Content of last fragments.tab' &&
+                if grep -q ^GCL '${output}'; then
+                    grep ^GCL '${output}' | cut -f 2- >> 'split/GC Content of last fragments.tab';
+                fi
             #end if
 
             #if 'gcc' in $outputs_to_split:
-                echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > "split/ACGT content per cycle.tab" &&
-                grep -q ^GCC "${output}" ; if [ $? = 0 ] ; then grep ^GCC "${output}" | cut -f 2- >> "split/ACGT content per cycle.tab" ; fi &&
+                && echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > 'split/ACGT content per cycle.tab' &&
+                if grep -q ^GCC '${output}'; then
+                    grep ^GCC '${output}' | cut -f 2- >> 'split/ACGT content per cycle.tab';
+                fi
             #end if
 
             #if 'is' in $outputs_to_split:
-                echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > "split/Insert sizes.tab" &&
-                grep -q ^IS  "${output}" ; if [ $? = 0 ] ; then grep ^IS  "${output}" | cut -f 2- >> "split/Insert sizes.tab"  ; fi &&
+                && echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > 'split/Insert sizes.tab' &&
+                if grep -q ^IS '${output}'; then
+                    grep ^IS '${output}' | cut -f 2- >> 'split/Insert sizes.tab';
+                fi
             #end if
 
             #if 'rl' in $outputs_to_split:
-                echo "# Read lengths. The columns are: read length, count" > "split/Read lengths.tab" &&
-                grep -q ^RL  "${output}" ; if [ $? = 0 ] ; then grep ^RL  "${output}" | cut -f 2- >> "split/Read lengths.tab"  ; fi &&
+                && echo "# Read lengths. The columns are: read length, count" > 'split/Read lengths.tab' &&
+                if grep -q ^RL '${output}'; then
+                    grep ^RL '${output}' | cut -f 2- >> 'split/Read lengths.tab';
+                fi
             #end if
 
             #if 'id' in $outputs_to_split:
-                echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > "split/Indel distribution.tab" &&
-                grep -q ^ID  "${output}" ; if [ $? = 0 ] ; then grep ^ID  "${output}" | cut -f 2- >> "split/Indel distribution.tab"  ; fi &&
+                && echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > 'split/Indel distribution.tab' &&
+                if grep -q ^ID '${output}'; then
+                    grep ^ID '${output}' | cut -f 2- >> 'split/Indel distribution.tab';
+                fi
             #end if
 
             #if 'ic' in $outputs_to_split:
-                echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" >  "split/Indels per cycle.tab"  &&
-                grep -q ^IC  "${output}" ; if [ $? = 0 ] ; then grep ^IC  "${output}" | cut -f 2- >> "split/Indels per cycle.tab"  ; fi &&
+                && echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" > 'split/Indels per cycle.tab' &&
+                if grep -q ^IC '${output}'; then
+                    grep ^IC '${output}' | cut -f 2- >> 'split/Indels per cycle.tab';
+                fi
             #end if
 
             #if 'cov' in $outputs_to_split:
-                echo "# Coverage distribution" > "split/Coverage distribution.tab" &&
-                grep -q ^COV "${output}" ; if [ $? = 0 ] ; then grep ^COV "${output}" | cut -f 2- >> "split/Coverage distribution.tab" ; fi &&
+                && echo "# Coverage distribution" > 'split/Coverage distribution.tab' &&
+                if grep -q ^COV '${output}'; then
+                    grep ^COV '${output}' | cut -f 2- >> 'split/Coverage distribution.tab';
+                fi
             #end if
 
             #if 'gcd' in $outputs_to_split:
-                echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > "split/GC depth.tab" &&
-                grep -q ^GCD "${output}" ; if [ $? = 0 ] ; then grep ^GCD "${output}" | cut -f 2- >> "split/GC depth.tab" ; fi &&
+                && echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > 'split/GC depth.tab' &&
+                if grep -q ^GCD '${output}'; then
+                    grep ^GCD '${output}' | cut -f 2- >> 'split/GC depth.tab';
+                fi
             #end if
-
-            ## Unix true command below
-
-            true
-
         #end if
         ]]></command>
     <inputs>
         <param name="input_file" type="data" format="sam,bam" label="BAM file" />
-        <param name="coverage_min" type="integer" value="1" label="Minimum coverage" help="minimum coverage value for --coverage option"/>
-        <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="maximum coverage value for --coverage option"/>
-        <param name="coverage_step" type="integer" value="1" label="Coverage step" help="step value for --coverage option"/>
-        <param name="remove_dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False" label="Exclude reads marked as duplicates" help="--remove-dups; default = False"/>
+        <param name="coverage_min" type="integer" value="1" label="Minimum coverage" help="Minimum coverage" />
+        <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="Maximum coverage" />
+        <param name="coverage_step" type="integer" value="1" label="Coverage step" help="Step value for coverage" />
+        <param name="remove_dups" argument="--remove-dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False"
+               label="Exclude reads marked as duplicates" />
         <conditional name="split_output">
-            <param name="split_output_selector" type="select" label="Output" help="Select between a single output or separate outputs for each statistics">
-                <option value="no" selected="True">a single summary file</option>
-                <option value="yes">separate datasets for each statistics</option>
+            <param name="split_output_selector" type="select" label="Output" help="Select between one single output or separate outputs for each statistics">
+                <option value="no" selected="True">One single summary file</option>
+                <option value="yes">Separate datasets for each statistic</option>
             </param>
             <when value="no" />
             <when value="yes">
-                <param name="generate_tables" type="select" display="checkboxes" multiple="True" label="Statistics to extract">
+                <param name="generate_tables" type="select" display="checkboxes" multiple="True" label="Desired output files">
                     <option value="sn">Summary numbers</option>
                     <option value="ffq">First Fragment Qualities</option>
                     <option value="lfq">Last Fragment Qualities</option>
@@ -156,12 +183,12 @@
             </when>
         </conditional>
         <conditional name="filter_by_flags">
-            <param name="filter_flags" type="select" label="Set filter by flags" help="-f and -F options">
+            <param name="filter_flags" type="select" label="Filter by SAM flags" help="More info on the flags: https://samtools.github.io/hts-specs/SAMv1.pdf">
                 <option value="nofilter" selected="True">Do not filter</option>
                 <option value="filter">Filter by flags to exclude or require</option>
             </param>
             <when value="filter">
-                <param name="require_flags" type="select" display="checkboxes" multiple="True" label="Require" help="-f">
+                <param name="require_flags" argument="-f" type="select" display="checkboxes" multiple="True" 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>
@@ -174,7 +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 name="exclude_flags" type="select" display="checkboxes" multiple="True" label="Exclude" help="-F">
+                <param name="exclude_flags" argument="-F" type="select" display="checkboxes" multiple="True" 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>
@@ -191,19 +218,18 @@
             <when value="nofilter" />
 
         </conditional>
-        <param name="gc_depth" type="float" value="20000" label="GC-depth bin size" help="--GC-depth; decreasing bin size increases memory requirement; default = 20000.0"/>
-        <param name="insert_size" type="integer" value="8000" label="Maximum insert size" help="--insert-size; default = 8000"/>
+        <param name="gc_depth" argument="--GC-depth" type="float" value="20000" label="Size of GC-depth bins" help="Decreasing bin size increases memory requirement" />
+        <param name="insert_size" argument="--insert-size" type="integer" value="8000" label="Maximum insert size" />
+        <!--
 
-        <!--
-            
             The -I option of samtools stats returns the following message in version 1.2:
 
             Samtools-htslib: init_group_id() header parsing not yet implemented
             Abort trap: 6
-    
+
             Because of this the section below is commented out until this stats bug is fixed
 
-            <param name="read_group" type="select" optional="true" label="Limit to a specific read group name" > 
+            <param name="read_group" type="select" optional="true" label="Limit to a specific read group name" >
                 <options>
                     <filter type="data_meta" ref="input_file" key="read_groups" />
                 </options>
@@ -211,12 +237,12 @@
 
         -->
 
-        <param name="read_length" type="integer" value="0" label="Minimum read length to generate statistics for" help="--read-length; default = no cutoff"/>
-        <param name="most_inserts" type="float" value="0.99" label="Report only the main part of inserts" help="--most-inserts; default = 0.99"/>
-        <param name="trim_quality" type="integer" value="0" label="BWA trim parameter" help="--trim-quality; default = 0"/>
-        
+        <param name="read_length" argument="--read-length" type="integer" value="" optional="true" label="Minimum read length to generate statistics for" help="No cutoff if left empty"/>
+        <param name="most_inserts" argument="--most-inserts" type="float" value="0.99" label="Report only the main part of inserts" />
+        <param name="trim_quality" argument="--trim-quality" type="integer" value="0" label="BWA trim parameter" />
+
         <conditional name="use_reference">
-            <param name="use_ref_selector" type="select" label="Use reference sequence" help="--ref-seq; required for GC-depth and mismatches-per-cycle calculation">
+            <param name="use_ref_selector" argument="--ref-seq" type="select" label="Use reference sequence" help="Required for GC-depth and mismatches-per-cycle calculation">
                 <option value="yes">Use reference</option>
                 <option selected="True" value="no">Do not use reference</option>
             </param>
@@ -228,8 +254,9 @@
                     </param>
                     <when value="cached">
                         <param name="ref_file" type="select" label="Using genome">
-                            <options from_data_table="fasta_indexes" />
-                            <filter type="data_meta" ref="input_file" key="dbkey" column="1" />
+                            <options from_data_table="fasta_indexes">
+                                <filter type="data_meta" ref="input_file" key="dbkey" column="1" />
+                            </options>
                         </param>
                     </when>
                     <when value="history">
@@ -243,7 +270,7 @@
     </inputs>
 
     <outputs>
-        <data format="tabular" name="output" label="${tool.name} on ${on_string}">
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}">
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tab" ext="tabular" visible="true" directory="split" />
         </data>
     </outputs>
@@ -263,34 +290,17 @@
             <param name="split_output_selector" value="yes" />
             <param name="generate_tables" value="sn,mpc,gcc" />
             <output name="output" file="samtools_stats_out2.tab" lines_diff="4">
-                <discovered_dataset designation="Summary numbers" ftype="tabular" file="samtools_stats_out2/sn.tab" />
-                <discovered_dataset designation="ACGT content per cycle" ftype="tabular" file="samtools_stats_out2/gcc.tab" />
-                <discovered_dataset designation="Mismatches per cycle" ftype="tabular" file="samtools_stats_out2/mpc.tab" />
+                <discovered_dataset designation="Summary numbers" ftype="tabular" file="samtools_stats_out2__sn.tab" />
+                <discovered_dataset designation="ACGT content per cycle" ftype="tabular" file="samtools_stats_out2__gcc.tab" />
+                <discovered_dataset designation="Mismatches per cycle" ftype="tabular" file="samtools_stats_out2__mpc.tab" />
             </output>
         </test>
     </tests>
     <help><![CDATA[
 **What it does**
 
-This tool runs the ``samtools stats`` command. It has the following options::
-
-    -c, --coverage <int>,<int>,<int>    Coverage distribution min,max,step [1,1000,1]
-    -d, --remove-dups                   Exclude from statistics reads marked as duplicates
-    -f, --required-flag  <str|int>      Required flag, 0 for unset. See also `samtools flags` [0]
-    -F, --filtering-flag <str|int>      Filtering flag, 0 for unset. See also `samtools flags` [0]
-        --GC-depth <float>              the size of GC-depth bins (decreasing bin size increases memory requirement) [2e4]
-    -h, --help                          This help message
-    -i, --insert-size <int>             Maximum insert size [8000]
-    -I, --id <string>                   Include only listed read group or sample name
-    -l, --read-length <int>             Include in the statistics only reads with the given read length []
-    -m, --most-inserts <float>          Report only the main part of inserts [0.99]
-    -q, --trim-quality <int>            The BWA trimming parameter [0]
-    -r, --ref-seq <file>                Reference sequence (required for GC-depth and mismatches-per-cycle calculation). Galaxy
-                                        will provide options for selecting a reference cached as this Galaxy instance or choosing
-                                        one from history.
-   
-
+This tool runs the ``samtools stats`` command.
     ]]></help>
-    <expand macro="citations"></expand>
+    <expand macro="citations"/>
 </tool>