--- a/sRNAPipe.xml	Thu Jul 12 08:24:21 2018 -0400
+++ b/sRNAPipe.xml	Thu Jul 12 08:27:08 2018 -0400
@@ -1,240 +1,240 @@
-<tool id="sRNAPipe" name="sRNAPipe" version="0.0.1">
-  <description>In-depth study of small RNA</description>
-  <command interpreter="perl">
-
-    ./bin/sRNAPipe.pl
-
-    --fastq ${first_input}
-    --fastq_n ${first_input.name}
-    #for $input_file in $input_files:
-    --fastq ${input_file.additional_input}
-    --fastq_n ${input_file.additional_input.name}
-    #end for
-
-    #if $Genome.refGenomeSource == "history":
-    --ref "${Genome.ownFile}"
-    --build_index
-    #else:
-    --ref "${Genome.indices.fields.path}"
-    #end if
-
-    #if $tRNAs.refGenomeSource == "history":
-    --tRNAs "${tRNAs.ownFile}"
-    --build_tRNAs
-    #elif $tRNAs.refGenomeSource == "none":
-    --tRNAs "None"
-    #else:
-    --tRNAs "${tRNAs.indices.fields.path}"
-    #end if
-
-    #if $snRNAs.refGenomeSource == "history":
-    --snRNAs "${snRNAs.ownFile}"
-    --build_snRNAs
-    #elif $snRNAs.refGenomeSource == "none":
-    --snRNAs "None"
-    #else:
-    --snRNAs "${snRNAs.indices.fields.path}"
-    #end if
-
-    #if $rRNAs.refGenomeSource == "history":
-    --rRNAs "${rRNAs.ownFile}"
-    --build_rRNAs
-    #elif $rRNAs.refGenomeSource == "none":
-    --rRNAs "None"
-    #else:
-    --rRNAs "${rRNAs.indices.fields.path}"
-    #end if
-
-    #if $miRNAs.refGenomeSource == "history":
-    --miRNAs "${miRNAs.ownFile}"
-    --build_miRNAs
-    #else:
-    --miRNAs "${miRNAs.indices.fields.path}"
-    #end if
-
-    #if $transcripts.refGenomeSource == "history":
-    --transcripts "${transcripts.ownFile}"
-    --build_transcripts
-    #else:
-    --transcripts "${transcripts.indices.fields.path}"
-    #end if
-
-    #if $TE.refGenomeSource == "history":
-    --TE "${TE.ownFile}"
-    --build_TE
-    #else:
-    --TE "${TE.indices.fields.path}"
-    #end if
-
-    --si_min $si_min
-    --si_max $si_max
-    --pi_min $pi_min
-    --pi_max $pi_max
-    --min $min
-    --max $max
-
-    --mis  $mis
-    --misTE $misTE
-    --dir $html_out.files_path
-    --html $html_out
-    --PPPon $PPPon
-  </command>
-
-  <requirements> 
-    <requirement type="package" version="0.7.15">bwa</requirement> 
-    <requirement type="package" version="2.26.0">bedtools</requirement> 
-    <requirement type="package" version="1.5">samtools</requirement> 
-  </requirements> 
-
-  <inputs>
-    <param format="fastqsanger" name="first_input" type="data" label="fastqsanger (Q33)" help=""/>
-    <repeat name="input_files" title="Additional Fastq Files">
-      <param format="fastqsanger" name="additional_input" type="data" label="fastqsanger (Q33)" help=""/>
-    </repeat>
-    <conditional name="Genome">
-      <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
-        <option value="indexed">Use a built-in index</option>
-        <option value="history">Use one from the history</option>
-      </param>
-      <when value="indexed">
-        <param name="indices" type="select" label="Select a reference genome">
-          <options from_data_table="bwa_indexes">
-            <filter type="sort_by" column="2" />
-            <validator type="no_options" message="No indexes are available" />
-          </options>
-        </param>
-      </when>
-      <when value="history">
-        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
-      </when>
-    </conditional>
-    <conditional name="transcripts">
-      <param name="refGenomeSource" type="select" label="Will you select transcripts database from your history or use a built-in index?">
-        <option value="indexed">Use a built-in index</option>
-        <option value="history">Use one from the history</option>
-      </param>
-      <when value="indexed">
-        <param name="indices" type="select" label="Select a transcripts reference">
-          <options from_data_table="bwa_indexes">
-            <filter type="sort_by" column="2" />
-            <validator type="no_options" message="No indexes are available" />
-          </options>
-        </param>
-      </when>
-      <when value="history">
-        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
-      </when>
-    </conditional>
-    <conditional name="TE">
-      <param name="refGenomeSource" type="select" label="Will you select TE database from your history or use a built-in index?">
-        <option value="indexed">Use a built-in index</option>
-        <option value="history">Use one from the history</option>
-      </param>
-      <when value="indexed">
-        <param name="indices" type="select" label="Select a TE reference">
-          <options from_data_table="bwa_indexes">
-            <filter type="sort_by" column="2" />
-            <validator type="no_options" message="No indexes are available" />
-          </options>
-        </param>
-      </when>
-      <when value="history">
-        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
-      </when>
-    </conditional>
-    <conditional name="miRNAs">
-      <param name="refGenomeSource" type="select" label="Will you select miRNA database from your history or use a built-in index?">
-        <option value="indexed">Use a built-in index</option>
-        <option value="history">Use one from the history</option>
-      </param>
-      <when value="indexed">
-        <param name="indices" type="select" label="Select a miRNA reference">
-          <options from_data_table="bwa_indexes">
-            <filter type="sort_by" column="2" />
-            <validator type="no_options" message="No indexes are available" />
-          </options>
-        </param>
-      </when>
-      <when value="history">
-        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
-      </when>
-    </conditional>
-    <conditional name="snRNAs">
-      <param name="refGenomeSource" type="select" label="Will you select snRNA database from your history or use a built-in index?">
-        <option value="indexed">Use a built-in index</option>
-        <option value="history">Use one from the history</option>
-        <option value="none">None</option>
-      </param>
-      <when value="indexed">
-        <param name="indices" type="select" label="Select a snRNAs reference">
-          <options from_data_table="bwa_indexes">
-            <filter type="sort_by" column="2" />
-            <validator type="no_options" message="No indexes are available" />
-          </options>
-        </param>
-      </when>
-      <when value="history">
-        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
-      </when>
-    </conditional>
-    <conditional name="rRNAs">
-      <param name="refGenomeSource" type="select" label="Will you select rRNAs database from your history or use a built-in index?">
-        <option value="indexed">Use a built-in index</option>
-        <option value="history">Use one from the history</option>
-        <option value="none">None</option>
-      </param>
-      <when value="indexed">
-        <param name="indices" type="select" label="Select a rRNAs reference">
-          <options from_data_table="bwa_indexes">
-            <filter type="sort_by" column="2" />
-            <validator type="no_options" message="No indexes are available" />
-          </options>
-        </param>
-      </when>
-      <when value="history">
-        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
-      </when>
-    </conditional>
-    <conditional name="tRNAs">
-      <param name="refGenomeSource" type="select" label="Will you select tRNA database from your history or use a built-in index?">
-        <option value="indexed">Use a built-in index</option>
-        <option value="history">Use one from the history</option>
-        <option value="none">None</option>
-      </param>
-      <when value="indexed">
-        <param name="indices" type="select" label="Select a tRNA reference">
-          <options from_data_table="bwa_indexes">
-            <filter type="sort_by" column="2" />
-            <validator type="no_options" message="No indexes are available" />
-          </options>
-        </param>
-      </when>
-      <when value="history">
-        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
-      </when>
-    </conditional>
-
-    <param name="min" type="integer" value="18" label="minimum read size"/>
-    <param name="max" type="integer" value="29" label="maximum read size"/>
-    <param name="si_min" type="integer" value="21" label="lower bound of siRNA range"/>  
-    <param name="si_max" type="integer" value="21" label="higher bound of siRNA range"/>
-    <param name="pi_min" type="integer" value="23" label="lower bound of piRNA range"/>
-    <param name="pi_max" type="integer" value="29" label="higher bound of piRNA range"/>
-
-    <param name="mis" type="integer" value="0" label="maximal genome mismatches"/>
-    <param name="misTE" type="integer" value="3" label="maximal TE mismatches"/>
-    <param name="PPPon" type="boolean" checked="true" label="PPPartners"/>
-  </inputs>
-  <outputs>
-    <data  format="html" name="html_out" label="${tool.name}_${first_input.name}_${on_string}"/>
-
-       <collection format ="fastqsanger" type="list" label="${tool.name}_fastq_outputs" name="output_fastqsanger">
-            <discover_datasets format ="fastqsanger" pattern="(?P&lt;name&gt;.*)" directory="fastq_dir" />
-        </collection>
-
-  </outputs>
-  <help>
- 	**User manual**
- 	"https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf"
-  </help>
-</tool>
+<tool id="sRNAPipe" name="sRNAPipe" version="0.0.1">
+  <description>In-depth study of small RNA</description>
+  <command interpreter="perl">
+
+    ./bin/sRNAPipe.pl
+
+    --fastq ${first_input}
+    --fastq_n ${first_input.name}
+    #for $input_file in $input_files:
+    --fastq ${input_file.additional_input}
+    --fastq_n ${input_file.additional_input.name}
+    #end for
+
+    #if $Genome.refGenomeSource == "history":
+    --ref "${Genome.ownFile}"
+    --build_index
+    #else:
+    --ref "${Genome.indices.fields.path}"
+    #end if
+
+    #if $tRNAs.refGenomeSource == "history":
+    --tRNAs "${tRNAs.ownFile}"
+    --build_tRNAs
+    #elif $tRNAs.refGenomeSource == "none":
+    --tRNAs "None"
+    #else:
+    --tRNAs "${tRNAs.indices.fields.path}"
+    #end if
+
+    #if $snRNAs.refGenomeSource == "history":
+    --snRNAs "${snRNAs.ownFile}"
+    --build_snRNAs
+    #elif $snRNAs.refGenomeSource == "none":
+    --snRNAs "None"
+    #else:
+    --snRNAs "${snRNAs.indices.fields.path}"
+    #end if
+
+    #if $rRNAs.refGenomeSource == "history":
+    --rRNAs "${rRNAs.ownFile}"
+    --build_rRNAs
+    #elif $rRNAs.refGenomeSource == "none":
+    --rRNAs "None"
+    #else:
+    --rRNAs "${rRNAs.indices.fields.path}"
+    #end if
+
+    #if $miRNAs.refGenomeSource == "history":
+    --miRNAs "${miRNAs.ownFile}"
+    --build_miRNAs
+    #else:
+    --miRNAs "${miRNAs.indices.fields.path}"
+    #end if
+
+    #if $transcripts.refGenomeSource == "history":
+    --transcripts "${transcripts.ownFile}"
+    --build_transcripts
+    #else:
+    --transcripts "${transcripts.indices.fields.path}"
+    #end if
+
+    #if $TE.refGenomeSource == "history":
+    --TE "${TE.ownFile}"
+    --build_TE
+    #else:
+    --TE "${TE.indices.fields.path}"
+    #end if
+
+    --si_min $si_min
+    --si_max $si_max
+    --pi_min $pi_min
+    --pi_max $pi_max
+    --min $min
+    --max $max
+
+    --mis  $mis
+    --misTE $misTE
+    --dir $html_out.files_path
+    --html $html_out
+    --PPPon $PPPon
+  </command>
+
+  <requirements> 
+    <requirement type="package" version="0.7.15">bwa</requirement> 
+    <requirement type="package" version="2.26.0">bedtools</requirement> 
+    <requirement type="package" version="1.5">samtools</requirement> 
+  </requirements> 
+
+  <inputs>
+    <param format="fastqsanger" name="first_input" type="data" label="fastqsanger (Q33)" help=""/>
+    <repeat name="input_files" title="Additional Fastq Files">
+      <param format="fastqsanger" name="additional_input" type="data" label="fastqsanger (Q33)" help=""/>
+    </repeat>
+    <conditional name="Genome">
+      <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
+        <option value="indexed">Use a built-in index</option>
+        <option value="history">Use one from the history</option>
+      </param>
+      <when value="indexed">
+        <param name="indices" type="select" label="Select a reference genome">
+          <options from_data_table="bwa_indexes">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
+      </when>
+    </conditional>
+    <conditional name="transcripts">
+      <param name="refGenomeSource" type="select" label="Will you select transcripts database from your history or use a built-in index?">
+        <option value="indexed">Use a built-in index</option>
+        <option value="history">Use one from the history</option>
+      </param>
+      <when value="indexed">
+        <param name="indices" type="select" label="Select a transcripts reference">
+          <options from_data_table="bwa_indexes">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
+      </when>
+    </conditional>
+    <conditional name="TE">
+      <param name="refGenomeSource" type="select" label="Will you select TE database from your history or use a built-in index?">
+        <option value="indexed">Use a built-in index</option>
+        <option value="history">Use one from the history</option>
+      </param>
+      <when value="indexed">
+        <param name="indices" type="select" label="Select a TE reference">
+          <options from_data_table="bwa_indexes">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
+      </when>
+    </conditional>
+    <conditional name="miRNAs">
+      <param name="refGenomeSource" type="select" label="Will you select miRNA database from your history or use a built-in index?">
+        <option value="indexed">Use a built-in index</option>
+        <option value="history">Use one from the history</option>
+      </param>
+      <when value="indexed">
+        <param name="indices" type="select" label="Select a miRNA reference">
+          <options from_data_table="bwa_indexes">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
+      </when>
+    </conditional>
+    <conditional name="snRNAs">
+      <param name="refGenomeSource" type="select" label="Will you select snRNA database from your history or use a built-in index?">
+        <option value="indexed">Use a built-in index</option>
+        <option value="history">Use one from the history</option>
+        <option value="none">None</option>
+      </param>
+      <when value="indexed">
+        <param name="indices" type="select" label="Select a snRNAs reference">
+          <options from_data_table="bwa_indexes">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
+      </when>
+    </conditional>
+    <conditional name="rRNAs">
+      <param name="refGenomeSource" type="select" label="Will you select rRNAs database from your history or use a built-in index?">
+        <option value="indexed">Use a built-in index</option>
+        <option value="history">Use one from the history</option>
+        <option value="none">None</option>
+      </param>
+      <when value="indexed">
+        <param name="indices" type="select" label="Select a rRNAs reference">
+          <options from_data_table="bwa_indexes">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
+      </when>
+    </conditional>
+    <conditional name="tRNAs">
+      <param name="refGenomeSource" type="select" label="Will you select tRNA database from your history or use a built-in index?">
+        <option value="indexed">Use a built-in index</option>
+        <option value="history">Use one from the history</option>
+        <option value="none">None</option>
+      </param>
+      <when value="indexed">
+        <param name="indices" type="select" label="Select a tRNA reference">
+          <options from_data_table="bwa_indexes">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
+      </when>
+    </conditional>
+
+    <param name="min" type="integer" value="18" label="minimum read size"/>
+    <param name="max" type="integer" value="29" label="maximum read size"/>
+    <param name="si_min" type="integer" value="21" label="lower bound of siRNA range"/>  
+    <param name="si_max" type="integer" value="21" label="higher bound of siRNA range"/>
+    <param name="pi_min" type="integer" value="23" label="lower bound of piRNA range"/>
+    <param name="pi_max" type="integer" value="29" label="higher bound of piRNA range"/>
+
+    <param name="mis" type="integer" value="0" label="maximal genome mismatches"/>
+    <param name="misTE" type="integer" value="3" label="maximal TE mismatches"/>
+    <param name="PPPon" type="boolean" checked="true" label="PPPartners"/>
+  </inputs>
+  <outputs>
+    <data  format="html" name="html_out" label="${tool.name}_${first_input.name}_${on_string}"/>
+
+       <collection format ="fastqsanger" type="list" label="${tool.name}_fastq_outputs" name="output_fastqsanger">
+            <discover_datasets format ="fastqsanger" pattern="(?P&lt;name&gt;.*)" directory="fastq_dir" />
+        </collection>
+
+  </outputs>
+  <help>
+ 	**User manual**
+ 	"https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf"
+  </help>
+</tool>