--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_stats.xml	Tue Sep 25 04:09:34 2018 -0400
@@ -0,0 +1,306 @@
+<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 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 '${use_reference.reference_source.ref_file}'` &&
+            #end if
+        #end if
+
+        samtools stats
+            '${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(',')])}
+                #end if
+            #end if
+
+            --GC-depth ${gc_depth}
+            --insert-size ${insert_size}
+
+            ## The code below is commented out because using -I/--id options causes the following exception
+            ## Samtools-htslib: init_group_id() header parsing not yet implemented
+            ##if str($read_group) != "":
+            ##    -I "${read_group}"
+            ##end if
+
+            #if str($read_length):
+                --read-length ${read_length}
+            #end if
+
+            --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}
+
+            #if 'sn' in $outputs_to_split:
+                && echo "# Summary Numbers" > 'split/Summary numbers.tab' &&
+                echo "" >> 'split/Summary numbers.tab' &&
+                if grep -q ^SN '${output}'; then
+                    grep ^SN '${output}' | cut -f 2- >> 'split/Summary numbers.tab';
+                fi
+            #end if
+
+            #if 'ffq' in $outputs_to_split:
+                && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > 'split/First Fragment Qualities.tab' &&
+                if grep -q ^FFQ '${output}'; then
+                    grep ^FFQ '${output}' | cut -f 2- >> 'split/First Fragment Qualities.tab';
+                fi
+            #end if
+
+            #if 'lfq' in $outputs_to_split:
+                && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > 'split/Last Fragment Qualities.tab' &&
+                if grep -q ^LFQ '${output}'; then
+                    grep ^LFQ '${output}' | cut -f 2- >> 'split/Last Fragment Qualities.tab';
+                fi
+            #end if
+
+            #if 'mpc' in $outputs_to_split:
+                && echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > 'split/Mismatches per cycle.tab' &&
+                if grep -q ^MPC '${output}'; then
+                    grep ^MPC '${output}' | cut -f 2- >> 'split/Mismatches per cycle.tab';
+                fi
+            #end if
+
+            #if 'gcf' in $outputs_to_split:
+                && echo "# GC Content of first fragments" > 'split/GC Content of first fragments.tab' &&
+                if grep -q ^GCF '${output}'; then
+                    grep ^GCF '${output}' | cut -f 2- >> 'split/GC Content of first fragments.tab';
+                fi
+            #end if
+
+            #if 'gcl' in $outputs_to_split:
+                && echo "# GC Content of last fragments" > 'split/GC Content of last fragments.tab' &&
+                if grep -q ^GCL '${output}'; then
+                    grep ^GCL '${output}' | cut -f 2- >> 'split/GC Content of last fragments.tab';
+                fi
+            #end if
+
+            #if 'gcc' in $outputs_to_split:
+                && echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > 'split/ACGT content per cycle.tab' &&
+                if grep -q ^GCC '${output}'; then
+                    grep ^GCC '${output}' | cut -f 2- >> 'split/ACGT content per cycle.tab';
+                fi
+            #end if
+
+            #if 'is' in $outputs_to_split:
+                && echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > 'split/Insert sizes.tab' &&
+                if grep -q ^IS '${output}'; then
+                    grep ^IS '${output}' | cut -f 2- >> 'split/Insert sizes.tab';
+                fi
+            #end if
+
+            #if 'rl' in $outputs_to_split:
+                && echo "# Read lengths. The columns are: read length, count" > 'split/Read lengths.tab' &&
+                if grep -q ^RL '${output}'; then
+                    grep ^RL '${output}' | cut -f 2- >> 'split/Read lengths.tab';
+                fi
+            #end if
+
+            #if 'id' in $outputs_to_split:
+                && echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > 'split/Indel distribution.tab' &&
+                if grep -q ^ID '${output}'; then
+                    grep ^ID '${output}' | cut -f 2- >> 'split/Indel distribution.tab';
+                fi
+            #end if
+
+            #if 'ic' in $outputs_to_split:
+                && echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" > 'split/Indels per cycle.tab' &&
+                if grep -q ^IC '${output}'; then
+                    grep ^IC '${output}' | cut -f 2- >> 'split/Indels per cycle.tab';
+                fi
+            #end if
+
+            #if 'cov' in $outputs_to_split:
+                && echo "# Coverage distribution" > 'split/Coverage distribution.tab' &&
+                if grep -q ^COV '${output}'; then
+                    grep ^COV '${output}' | cut -f 2- >> 'split/Coverage distribution.tab';
+                fi
+            #end if
+
+            #if 'gcd' in $outputs_to_split:
+                && echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > 'split/GC depth.tab' &&
+                if grep -q ^GCD '${output}'; then
+                    grep ^GCD '${output}' | cut -f 2- >> 'split/GC depth.tab';
+                fi
+            #end if
+        #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" />
+        <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 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="Desired output files">
+                    <option value="sn">Summary numbers</option>
+                    <option value="ffq">First Fragment Qualities</option>
+                    <option value="lfq">Last Fragment Qualities</option>
+                    <option value="mpc">Mismatches per cycle</option>
+                    <option value="gcf">GC Content of first fragments</option>
+                    <option value="gcl">GC Content of last fragments</option>
+                    <option value="gcc">ACGT content per cycle</option>
+                    <option value="is">Insert sizes</option>
+                    <option value="rl">Read lengths</option>
+                    <option value="id">Indel distribution</option>
+                    <option value="ic">Indels per cycle</option>
+                    <option value="cov">Coverage distribution</option>
+                    <option value="gcd">GC depth</option>
+                </param>
+            </when>
+        </conditional>
+        <conditional name="filter_by_flags">
+            <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" 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>
+                    <option value="8">The mate is unmapped</option>
+                    <option value="16">Read strand</option>
+                    <option value="32">Mate strand</option>
+                    <option value="64">Read is the first in a pair</option>
+                    <option value="128">Read is the second in a pair</option>
+                    <option value="256">The alignment or this read is not primary</option>
+                    <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" 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>
+                    <option value="8">The mate is unmapped</option>
+                    <option value="16">Read strand</option>
+                    <option value="32">Mate strand</option>
+                    <option value="64">Read is the first in a pair</option>
+                    <option value="128">Read is the second in a pair</option>
+                    <option value="256">The alignment or this read is not primary</option>
+                    <option value="512">The read fails platform/vendor quality checks</option>
+                    <option value="1024">The read is a PCR or optical duplicate</option>
+                </param>
+            </when>
+            <when value="nofilter" />
+
+        </conditional>
+        <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" >
+                <options>
+                    <filter type="data_meta" ref="input_file" key="read_groups" />
+                </options>
+            </param>
+
+        -->
+
+        <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" 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>
+            <when value="yes">
+                <conditional name="reference_source">
+                    <param name="reference_source_selector" type="select" label="Choose a reference sequence for GC depth">
+                        <option value="cached">Locally cached</option>
+                        <option value="history">History</option>
+                    </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>
+                        </param>
+                    </when>
+                    <when value="history">
+                        <param name="ref_file" type="data" format="fasta" label="Using file" />
+                    </when>
+                </conditional>
+            </when>
+            <when value="no" />
+        </conditional>
+
+    </inputs>
+
+    <outputs>
+        <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>
+    <tests>
+        <test>
+            <param name="input_file" value="samtools_stats_input.bam" ftype="bam" />
+            <param name="use_ref_selector" value="yes" />
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" />
+            <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="4" />
+        </test>
+        <test>
+            <param name="input_file" value="samtools_stats_input.bam" ftype="bam" />
+            <param name="use_ref_selector" value="yes" />
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" />
+            <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" />
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool runs the ``samtools stats`` command.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
+