diff picard_ValidateSamFile.xml @ 33:3f254c5ced1d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
children
line wrap: on
line diff
--- a/picard_ValidateSamFile.xml	Mon Sep 25 08:32:17 2023 +0000
+++ b/picard_ValidateSamFile.xml	Sun Mar 03 16:06:11 2024 +0000
@@ -1,14 +1,14 @@
-<tool name="ValidateSamFile" id="picard_ValidateSamFile" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
-  <description>assess validity of SAM/BAM dataset</description>
-  <macros>
-    <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">2</token>
-  </macros>
-  <expand macro="requirements" />
-  <stdio>
-    <exit_code range="1:"  level="warning"/>
-  </stdio>
-  <command><![CDATA[
+<tool name="ValidateSamFile" id="picard_ValidateSamFile" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
+    <description>assess validity of SAM/BAM dataset</description>
+    <macros>
+        <import>picard_macros.xml</import>
+        <token name="@WRAPPER_VERSION@">0</token>
+    </macros>
+    <expand macro="requirements"/>
+    <stdio>
+        <exit_code range="1:" level="warning"/>
+    </stdio>
+    <command><![CDATA[
 
     ##set the maximum number of open file to hard maximum or 4096 if on a mac (mac gives 'unlimited' as output of `ulimit -Hn` command
 
@@ -21,148 +21,141 @@
     #set $reference_fasta_filename = "localref.fa"
 
     #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
+        ln -sf '${reference_source.ref_file}' '${reference_fasta_filename}' &&
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
 
     @java_options@
 
-    picard
-    ValidateSamFile
+    picard ValidateSamFile
 
-    INPUT='$escaped_element_identifier'
-    OUTPUT="${outFile}"
-    MODE="${mode}"
+    --INPUT '$escaped_element_identifier'
+    --OUTPUT '${outFile}'
+    --MODE '${mode}'
 
     #if str( $ignore ) != "None":
       #for $element in str( $ignore ).split(','):   ## See trello card https://trello.com/c/9nW02Zhd
-        IGNORE="${element}"
+        --IGNORE '${element}'
       #end for
     #end if
 
-    MAX_OUTPUT="${max_output}"
-    REFERENCE_SEQUENCE="${reference_fasta_filename}"
-    IGNORE_WARNINGS="${ignore_warnings}"
-    IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}"
-    VALIDATE_INDEX="${validate_index}"
-    MAX_OPEN_TEMP_FILES=`ulimit -Sn`
+    --MAX_OUTPUT '${max_output}'
+    --REFERENCE_SEQUENCE '${reference_fasta_filename}'
+    --IGNORE_WARNINGS '${ignore_warnings}'
+    --IS_BISULFITE_SEQUENCED '${is_bisulfite_sequenced}'
+    --MAX_OPEN_TEMP_FILES `ulimit -Sn`
 
-    VERBOSITY=ERROR
-    QUIET=true
+    --VERBOSITY ERROR
+    --QUIET true
 
   ]]></command>
-  <inputs>
-    <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset." />
-     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Load reference genome from">
-        <option value="cached">Local cache</option>
-        <option value="history">History</option>
-      </param>
-      <when value="cached">
-        <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
-          <options from_data_table="picard_indexes">
-            <filter type="sort_by" column="2" />
-            <validator type="no_options" message="No indexes are available" />
-          </options>
-          <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
+    <inputs>
+        <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Load reference genome from">
+                <option value="cached">Local cache</option>
+                <option value="history">History</option>
+            </param>
+            <when value="cached">
+                <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
+                    <options from_data_table="picard_indexes">
+                        <filter type="sort_by" column="2"/>
+                        <validator type="no_options" message="No indexes are available"/>
+                    </options>
+                    <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command"/>
+            </when>
+        </conditional>
+        <param name="mode" type="select" label="Select output mode" help="MODE">
+            <option value="VERBOSE">Verbose</option>
+            <option value="SUMMARY">Summary</option>
         </param>
-      </when>
-      <when value="history">
-        <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" />
-      </when>
-    </conditional>
-
-    <param name="mode" type="select" label="Select output mode" help="MODE">
-      <option value="VERBOSE">Verbose</option>
-      <option value="SUMMARY">Summary</option>
-    </param>
-    <param name="ignore" type="select" multiple="true" display="checkboxes" label="Select validation error types to ignore" help="IGNORE">
-      <option value="INVALID_QUALITY_FORMAT">INVALID_QUALITY_FORMAT</option>
-      <option value="INVALID_FLAG_PROPER_PAIR">INVALID_FLAG_PROPER_PAIR</option>
-      <option value="INVALID_FLAG_MATE_UNMAPPED">INVALID_FLAG_MATE_UNMAPPED</option>
-      <option value="MISMATCH_FLAG_MATE_UNMAPPED">MISMATCH_FLAG_MATE_UNMAPPED</option>
-      <option value="INVALID_FLAG_MATE_NEG_STRAND">INVALID_FLAG_MATE_NEG_STRAND</option>
-      <option value="MISMATCH_FLAG_MATE_NEG_STRAND">MISMATCH_FLAG_MATE_NEG_STRAND</option>
-      <option value="INVALID_FLAG_FIRST_OF_PAIR">INVALID_FLAG_FIRST_OF_PAIR</option>
-      <option value="INVALID_FLAG_SECOND_OF_PAIR">INVALID_FLAG_SECOND_OF_PAIR</option>
-      <option value="PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND">PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND</option>
-      <option value="INVALID_FLAG_NOT_PRIM_ALIGNMENT">INVALID_FLAG_NOT_PRIM_ALIGNMENT</option>
-      <option value="INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT">INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT</option>
-      <option value="INVALID_FLAG_READ_UNMAPPED">INVALID_FLAG_READ_UNMAPPED</option>
-      <option value="INVALID_INSERT_SIZE">INVALID_INSERT_SIZE</option>
-      <option value="INVALID_MAPPING_QUALITY">INVALID_MAPPING_QUALITY</option>
-      <option value="INVALID_CIGAR">INVALID_CIGAR</option>
-      <option value="ADJACENT_INDEL_IN_CIGAR">ADJACENT_INDEL_IN_CIGAR</option>
-      <option value="INVALID_MATE_REF_INDEX">INVALID_MATE_REF_INDEX</option>
-      <option value="MISMATCH_MATE_REF_INDEX">MISMATCH_MATE_REF_INDEX</option>
-      <option value="INVALID_REFERENCE_INDEX">INVALID_REFERENCE_INDEX</option>
-      <option value="INVALID_ALIGNMENT_START">INVALID_ALIGNMENT_START</option>
-      <option value="MISMATCH_MATE_ALIGNMENT_START">MISMATCH_MATE_ALIGNMENT_START</option>
-      <option value="MATE_FIELD_MISMATCH">MATE_FIELD_MISMATCH</option>
-      <option value="INVALID_TAG_NM">INVALID_TAG_NM</option>
-      <option value="MISSING_TAG_NM">MISSING_TAG_NM</option>
-      <option value="MISSING_HEADER">MISSING_HEADER</option>
-      <option value="MISSING_SEQUENCE_DICTIONARY">MISSING_SEQUENCE_DICTIONARY</option>
-      <option value="MISSING_READ_GROUP">MISSING_READ_GROUP</option>
-      <option value="RECORD_OUT_OF_ORDER">RECORD_OUT_OF_ORDER</option>
-      <option value="READ_GROUP_NOT_FOUND">READ_GROUP_NOT_FOUND</option>
-      <option value="RECORD_MISSING_READ_GROUP">RECORD_MISSING_READ_GROUP</option>
-      <option value="INVALID_INDEXING_BIN">INVALID_INDEXING_BIN</option>
-      <option value="MISSING_VERSION_NUMBER">MISSING_VERSION_NUMBER</option>
-      <option value="INVALID_VERSION_NUMBER">INVALID_VERSION_NUMBER</option>
-      <option value="TRUNCATED_FILE">TRUNCATED_FILE</option>
-      <option value="MISMATCH_READ_LENGTH_AND_QUALS_LENGTH">MISMATCH_READ_LENGTH_AND_QUALS_LENGTH</option>
-      <option value="EMPTY_READ">EMPTY_READ</option>
-      <option value="CIGAR_MAPS_OFF_REFERENCE">CIGAR_MAPS_OFF_REFERENCE</option>
-      <option value="MISMATCH_READ_LENGTH_AND_E2_LENGTH">MISMATCH_READ_LENGTH_AND_E2_LENGTH</option>
-      <option value="MISMATCH_READ_LENGTH_AND_U2_LENGTH">MISMATCH_READ_LENGTH_AND_U2_LENGTH</option>
-      <option value="E2_BASE_EQUALS_PRIMARY_BASE">E2_BASE_EQUALS_PRIMARY_BASE</option>
-      <option value="BAM_FILE_MISSING_TERMINATOR_BLOCK">BAM_FILE_MISSING_TERMINATOR_BLOCK</option>
-      <option value="UNRECOGNIZED_HEADER_TYPE">UNRECOGNIZED_HEADER_TYPE</option>
-      <option value="POORLY_FORMATTED_HEADER_TAG">POORLY_FORMATTED_HEADER_TAG</option>
-      <option value="HEADER_TAG_MULTIPLY_DEFINED">HEADER_TAG_MULTIPLY_DEFINED</option>
-      <option value="HEADER_RECORD_MISSING_REQUIRED_TAG">HEADER_RECORD_MISSING_REQUIRED_TAG</option>
-      <option value="INVALID_DATE_STRING">INVALID_DATE_STRING</option>
-      <option value="TAG_VALUE_TOO_LARGE">TAG_VALUE_TOO_LARGE</option>
-      <option value="INVALID_INDEX_FILE_POINTER">INVALID_INDEX_FILE_POINTER</option>
-      <option value="INVALID_PREDICTED_MEDIAN_INSERT_SIZE">INVALID_PREDICTED_MEDIAN_INSERT_SIZE</option>
-      <option value="DUPLICATE_READ_GROUP_ID">DUPLICATE_READ_GROUP_ID</option>
-      <option value="MISSING_PLATFORM_VALUE">MISSING_PLATFORM_VALUE</option>
-      <option value="INVALID_PLATFORM_VALUE">INVALID_PLATFORM_VALUE</option>
-      <option value="DUPLICATE_PROGRAM_GROUP_ID">DUPLICATE_PROGRAM_GROUP_ID</option>
-      <option value="MATE_NOT_FOUND">MATE_NOT_FOUND</option>
-      <option value="MATES_ARE_SAME_END">MATES_ARE_SAME_END</option>
-      <option value="MISMATCH_MATE_CIGAR_STRING">MISMATCH_MATE_CIGAR_STRING</option>
-      <option value="MATE_CIGAR_STRING_INVALID_PRESENCE">MATE_CIGAR_STRING_INVALID_PRESENCE</option>
-    </param>
-    <param name="max_output" type="integer" value="100" label="The maximum number of lines output in verbose mode" help="MAX_OUTPUT; default=100"/>
-    <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/>
-    <param name="validate_index" type="boolean" checked="True" label="If true and input is a BAM file with an index file, also validates the index" help="VALIDATE_INDEX; default=True"/>
-    <param name="is_bisulfite_sequenced" type="boolean" label="Whether the SAM or BAM file consists of bisulfite sequenced reads" help="IS_BISULFITE_SEQUENCED; If so, C->T is not counted as an error in computing the value of the NM tag; default=False"/>
-
-  </inputs>
-
-  <outputs>
-    <data format="txt" name="outFile" label="${tool.name} on ${on_string}: BAM validation summary"/>
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="inputFile" value="picard_ValidateSamFile.bam" ftype="bam"/>
-      <param name="reference_source_selector" value="history"/>
-      <param name="ref_file" value="picard_ValidateSamFile_ref.fa"/>
-      <param name="mode" value="VERBOSE"/>
-      <param name="ignore" value="INVALID_QUALITY_FORMAT,INVALID_FLAG_PROPER_PAIR"/>
-      <param name="max_output" value="100"/>
-      <param name="ignore_warnings" value="Fasle"/>
-      <param name="validate_index" value="True"/>
-      <param name="is_bisulfite_sequenced" value="False"/>
-      <output name="outFile" file="picard_ValidateSamFile_test1.txt" ftype="txt"/>
-    </test>
-  </tests>
-
-  <help>
+        <param name="ignore" type="select" multiple="true" display="checkboxes" label="Select validation error types to ignore" help="IGNORE">
+            <option value="INVALID_QUALITY_FORMAT">INVALID_QUALITY_FORMAT</option>
+            <option value="INVALID_FLAG_PROPER_PAIR">INVALID_FLAG_PROPER_PAIR</option>
+            <option value="INVALID_FLAG_MATE_UNMAPPED">INVALID_FLAG_MATE_UNMAPPED</option>
+            <option value="MISMATCH_FLAG_MATE_UNMAPPED">MISMATCH_FLAG_MATE_UNMAPPED</option>
+            <option value="INVALID_FLAG_MATE_NEG_STRAND">INVALID_FLAG_MATE_NEG_STRAND</option>
+            <option value="MISMATCH_FLAG_MATE_NEG_STRAND">MISMATCH_FLAG_MATE_NEG_STRAND</option>
+            <option value="INVALID_FLAG_FIRST_OF_PAIR">INVALID_FLAG_FIRST_OF_PAIR</option>
+            <option value="INVALID_FLAG_SECOND_OF_PAIR">INVALID_FLAG_SECOND_OF_PAIR</option>
+            <option value="PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND">PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND</option>
+            <option value="INVALID_FLAG_NOT_PRIM_ALIGNMENT">INVALID_FLAG_NOT_PRIM_ALIGNMENT</option>
+            <option value="INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT">INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT</option>
+            <option value="INVALID_FLAG_READ_UNMAPPED">INVALID_FLAG_READ_UNMAPPED</option>
+            <option value="INVALID_INSERT_SIZE">INVALID_INSERT_SIZE</option>
+            <option value="INVALID_MAPPING_QUALITY">INVALID_MAPPING_QUALITY</option>
+            <option value="INVALID_CIGAR">INVALID_CIGAR</option>
+            <option value="ADJACENT_INDEL_IN_CIGAR">ADJACENT_INDEL_IN_CIGAR</option>
+            <option value="INVALID_MATE_REF_INDEX">INVALID_MATE_REF_INDEX</option>
+            <option value="MISMATCH_MATE_REF_INDEX">MISMATCH_MATE_REF_INDEX</option>
+            <option value="INVALID_REFERENCE_INDEX">INVALID_REFERENCE_INDEX</option>
+            <option value="INVALID_ALIGNMENT_START">INVALID_ALIGNMENT_START</option>
+            <option value="MISMATCH_MATE_ALIGNMENT_START">MISMATCH_MATE_ALIGNMENT_START</option>
+            <option value="MATE_FIELD_MISMATCH">MATE_FIELD_MISMATCH</option>
+            <option value="INVALID_TAG_NM">INVALID_TAG_NM</option>
+            <option value="MISSING_TAG_NM">MISSING_TAG_NM</option>
+            <option value="MISSING_HEADER">MISSING_HEADER</option>
+            <option value="MISSING_SEQUENCE_DICTIONARY">MISSING_SEQUENCE_DICTIONARY</option>
+            <option value="MISSING_READ_GROUP">MISSING_READ_GROUP</option>
+            <option value="RECORD_OUT_OF_ORDER">RECORD_OUT_OF_ORDER</option>
+            <option value="READ_GROUP_NOT_FOUND">READ_GROUP_NOT_FOUND</option>
+            <option value="RECORD_MISSING_READ_GROUP">RECORD_MISSING_READ_GROUP</option>
+            <option value="INVALID_INDEXING_BIN">INVALID_INDEXING_BIN</option>
+            <option value="MISSING_VERSION_NUMBER">MISSING_VERSION_NUMBER</option>
+            <option value="INVALID_VERSION_NUMBER">INVALID_VERSION_NUMBER</option>
+            <option value="TRUNCATED_FILE">TRUNCATED_FILE</option>
+            <option value="MISMATCH_READ_LENGTH_AND_QUALS_LENGTH">MISMATCH_READ_LENGTH_AND_QUALS_LENGTH</option>
+            <option value="EMPTY_READ">EMPTY_READ</option>
+            <option value="CIGAR_MAPS_OFF_REFERENCE">CIGAR_MAPS_OFF_REFERENCE</option>
+            <option value="MISMATCH_READ_LENGTH_AND_E2_LENGTH">MISMATCH_READ_LENGTH_AND_E2_LENGTH</option>
+            <option value="MISMATCH_READ_LENGTH_AND_U2_LENGTH">MISMATCH_READ_LENGTH_AND_U2_LENGTH</option>
+            <option value="E2_BASE_EQUALS_PRIMARY_BASE">E2_BASE_EQUALS_PRIMARY_BASE</option>
+            <option value="BAM_FILE_MISSING_TERMINATOR_BLOCK">BAM_FILE_MISSING_TERMINATOR_BLOCK</option>
+            <option value="UNRECOGNIZED_HEADER_TYPE">UNRECOGNIZED_HEADER_TYPE</option>
+            <option value="POORLY_FORMATTED_HEADER_TAG">POORLY_FORMATTED_HEADER_TAG</option>
+            <option value="HEADER_TAG_MULTIPLY_DEFINED">HEADER_TAG_MULTIPLY_DEFINED</option>
+            <option value="HEADER_RECORD_MISSING_REQUIRED_TAG">HEADER_RECORD_MISSING_REQUIRED_TAG</option>
+            <option value="INVALID_DATE_STRING">INVALID_DATE_STRING</option>
+            <option value="TAG_VALUE_TOO_LARGE">TAG_VALUE_TOO_LARGE</option>
+            <option value="INVALID_INDEX_FILE_POINTER">INVALID_INDEX_FILE_POINTER</option>
+            <option value="INVALID_PREDICTED_MEDIAN_INSERT_SIZE">INVALID_PREDICTED_MEDIAN_INSERT_SIZE</option>
+            <option value="DUPLICATE_READ_GROUP_ID">DUPLICATE_READ_GROUP_ID</option>
+            <option value="MISSING_PLATFORM_VALUE">MISSING_PLATFORM_VALUE</option>
+            <option value="INVALID_PLATFORM_VALUE">INVALID_PLATFORM_VALUE</option>
+            <option value="DUPLICATE_PROGRAM_GROUP_ID">DUPLICATE_PROGRAM_GROUP_ID</option>
+            <option value="MATE_NOT_FOUND">MATE_NOT_FOUND</option>
+            <option value="MATES_ARE_SAME_END">MATES_ARE_SAME_END</option>
+            <option value="MISMATCH_MATE_CIGAR_STRING">MISMATCH_MATE_CIGAR_STRING</option>
+            <option value="MATE_CIGAR_STRING_INVALID_PRESENCE">MATE_CIGAR_STRING_INVALID_PRESENCE</option>
+        </param>
+        <param name="max_output" type="integer" value="100" label="The maximum number of lines output in verbose mode" help="MAX_OUTPUT; default=100"/>
+        <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/>
+        <param name="validate_index" type="boolean" checked="True" label="If true and input is a BAM file with an index file, also validates the index" help="VALIDATE_INDEX; default=True"/>
+        <param name="is_bisulfite_sequenced" type="boolean" label="Whether the SAM or BAM file consists of bisulfite sequenced reads" help="IS_BISULFITE_SEQUENCED; If so, C-&gt;T is not counted as an error in computing the value of the NM tag; default=False"/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="outFile" label="${tool.name} on ${on_string}: BAM validation summary"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputFile" value="picard_ValidateSamFile.bam" ftype="bam"/>
+            <param name="reference_source_selector" value="history"/>
+            <param name="ref_file" value="picard_ValidateSamFile_ref.fa"/>
+            <param name="mode" value="VERBOSE"/>
+            <param name="ignore" value="INVALID_QUALITY_FORMAT,INVALID_FLAG_PROPER_PAIR"/>
+            <param name="max_output" value="100"/>
+            <param name="ignore_warnings" value="Fasle"/>
+            <param name="validate_index" value="True"/>
+            <param name="is_bisulfite_sequenced" value="False"/>
+            <output name="outFile" file="picard_ValidateSamFile_test1.txt" ftype="txt"/>
+        </test>
+    </tests>
+    <help>
 
 **Purpose**
 
@@ -215,12 +208,12 @@
                                 values: {true, false}
 
   IS_BISULFITE_SEQUENCED=Boolean
-  BISULFITE=Boolean             Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not
+  BISULFITE=Boolean             Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C-&gt;T is not
                                 counted as an error in computing the value of the NM tag.  Default value: false. This
                                 option can be set to 'null' to clear the default value. Possible values: {true, false}
 
 @more_info@
 
   </help>
-  <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>