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annotate picard_SamToFastq.xml @ 33:3f254c5ced1d draft default tip

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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
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1 <tool name="SamToFastq" id="picard_SamToFastq" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
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2 <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 <token name="@WRAPPER_VERSION@">0</token>
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6 </macros>
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7 <xrefs>
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8 <xref type="bio.tools">picard_samtofastq</xref>
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9 </xrefs>
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10 <expand macro="requirements"/>
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11 <command detect_errors="exit_code"><![CDATA[
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13 @java_options@
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14 @symlink_element_identifier@
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16 picard SamToFastq
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18 --INPUT '$escaped_element_identifier'
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20 #if str($single_or_paired) == "pe_interleaved":
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21 --FASTQ '${interleaved_fastq}'
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22 --INTERLEAVE TRUE
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23 #else if str($single_or_paired) == "pe_sep":
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24 --F '${fq1}'
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25 --F2 '${fq2}'
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26 --FU '${fq_u}'
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27 #else
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28 --F '${fq_single}'
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29 #end if
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31 --RE_REVERSE '${re_reverse}'
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33 -INCLUDE_NON_PF_READS '${include_non_pf_reads}'
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34 #if len(str($clipping_attribute)) > 0:
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35 --CLIPPING_ATTRIBUTE '${clipping_attribute}'
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36 #end if
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37 #if len(str($clipping_action)) > 0:
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38 --CLIPPING_ACTION '${clipping_action}'
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39 #end if
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40 --READ1_TRIM '${read1_trim}'
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42 #if int($read1_max_bases_to_write) > -1:
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43 --READ1_MAX_BASES_TO_WRITE '${read1_max_bases_to_write}'
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44 #end if
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46 --READ2_TRIM '${read2_trim}'
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48 #if int($read2_max_bases_to_write) > -1:
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49 --READ2_MAX_BASES_TO_WRITE '${read2_max_bases_to_write}'
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50 #end if
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52 --INCLUDE_NON_PRIMARY_ALIGNMENTS '${include_non_primary_alignments}'
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54 --VALIDATION_STRINGENCY '${validation_stringency}'
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55 --QUIET true
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56 --VERBOSITY ERROR
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57
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58 ]]></command>
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59 <inputs>
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60 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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61 <param name="single_or_paired" type="select" label="Output format">
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62 <option value="se">Single-end</option>
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63 <option value="pe_interleaved" selected="true">Paired-end (one interleaved output file)</option>
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64 <option value="pe_sep">Paired-end (two separate output files)</option>
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65 </param>
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66 <param name="re_reverse" type="boolean" checked="True" label="Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq" help="RE_REVERSE; default=True"/>
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67 <param name="include_non_pf_reads" type="boolean" label="Include non-PF reads from the SAM/BAM dataset into the output FASTQ" help="INCLUDE_NON_PF_READS; PF means 'passes filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads; default=False"/>
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68 <param name="clipping_attribute" type="text" value="" label="The attribute that stores the position at which the SAM/BAM record should be clipped" help="CLIPPING_ATTRIBUTE; default=null"/>
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69 <param name="clipping_action" type="text" value="" label="The action that should be taken with clipped reads: 'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region" help="CLIPPING_ACTION; default=null"/>
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70 <param name="read1_trim" type="integer" value="0" min="0" label="The number of bases to trim from the beginning of read 1" help="READ1_TRIM; default=0"/>
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71 <param name="read1_max_bases_to_write" type="integer" value="-1" label="The maximum number of bases to write from read 1 after trimming" help="READ1_MAX_BASES_TO_WRITE; If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written; default=null (-1)"/>
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72 <param name="read2_trim" type="integer" value="0" min="0" label="The number of bases to trim from the beginning of read 2" help="READ2_TRIM; default=0"/>
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73 <param name="read2_max_bases_to_write" type="integer" value="-1" label="The maximum number of bases to write from read 2 after trimming" help="READ2_MAX_BASES_TO_WRITE; If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written; default=null (-1)"/>
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74 <param name="include_non_primary_alignments" type="boolean" label="If true, include non-primary alignments in the output" help="INCLUDE_NON_PRIMARY_ALIGNMENTS; Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments; default=False"/>
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75 <expand macro="VS"/>
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76 </inputs>
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77 <outputs>
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78 <data format="fastqsanger" name="fq_single" label="${tool.name} on ${on_string}: reads as fastq">
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79 <filter>output_type['single_or_paired'] == 'se'</filter>
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80 </data>
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81 <data format="fastqsanger" name="interleaved_fastq" label="Interleaved pairs from ${tool.name} on ${on_string}">
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82 <filter>output_type['single_or_paired'] == 'pe_interleaved'</filter>
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83 </data>
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84 <data format="fastqsanger" name="fq1" label="Paired-end forward strand from ${tool.name} on ${on_string}">
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85 <filter>output_type['single_or_paired'] == 'pe_sep'</filter>
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86 </data>
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87 <data format="fastqsanger" name="fq2" label="Paired-end reverse strand from ${tool.name} on ${on_string}">
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88 <filter>output_type['single_or_paired'] == 'pe_sep'</filter>
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89 </data>
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90 <data format="fastqsanger" name="fq_u" label="Paired-end unpaired reads from ${tool.name} on ${on_string}">
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91 <filter>output_type['single_or_paired'] == 'pe_sep'</filter>
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92 </data>
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93 </outputs>
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94 <tests>
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95 <test expect_num_outputs="5">
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96 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
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97 <param name="single_or_paired" value="pe_interleaved"/>
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98 <param name="re_reverse" value="true"/>
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99 <param name="include_non_pf_reads" value="false"/>
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100 <param name="clipping_attribute" value=""/>
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101 <param name="clipping_action" value=""/>
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102 <param name="read1_trim" value="0"/>
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103 <param name="read1_max_bases_to_write" value="-1"/>
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104 <param name="read2_trim" value="0"/>
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105 <param name="read2_max_bases_to_write" value="-1"/>
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106 <param name="include_non_primary_alignments" value="false"/>
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107 <output name="interleaved_fastq" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/>
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108 </test>
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109 <test expect_num_outputs="5">
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110 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
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111 <param name="single_or_paired" value="pe_sep"/>
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112 <param name="re_reverse" value="true"/>
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113 <param name="include_non_pf_reads" value="false"/>
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114 <param name="clipping_attribute" value=""/>
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115 <param name="clipping_action" value=""/>
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116 <param name="read1_trim" value="0"/>
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117 <param name="read1_max_bases_to_write" value="-1"/>
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118 <param name="read2_trim" value="0"/>
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119 <param name="read2_max_bases_to_write" value="-1"/>
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120 <param name="include_non_primary_alignments" value="false"/>
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121 <output name="fq1" file="picard_SamToFastq_1.fq" ftype="fastqsanger"/>
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122 <output name="fq2" file="picard_SamToFastq_2.fq" ftype="fastqsanger"/>
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123 <output name="fq_u" file="picard_SamToFastq_u.fq" ftype="fastqsanger"/>
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124 </test>
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125 <test expect_num_outputs="5">
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126 <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/>
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127 <param name="single_or_paired" value="se"/>
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128 <param name="re_reverse" value="true"/>
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129 <param name="include_non_pf_reads" value="false"/>
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130 <param name="clipping_attribute" value=""/>
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131 <param name="clipping_action" value=""/>
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132 <param name="read1_trim" value="0"/>
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133 <param name="read1_max_bases_to_write" value="-1"/>
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134 <param name="read2_trim" value="0"/>
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135 <param name="read2_max_bases_to_write" value="-1"/>
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136 <param name="include_non_primary_alignments" value="false"/>
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137 <output name="fq_single" file="picard_SamToFastq_se.fq" ftype="fastqsanger"/>
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138 </test>
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139 </tests>
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140 <help>
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141
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142 **Purpose**
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143
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144 Extracts read sequences and qualities from the input SAM/BAM dataset and outputs them in Sanger fastq format. In the RE_REVERSE=True mode (default behavior), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM.BAM dataset will be reverse-complemented prior to writing it to fastq in order restore correctly the original read sequence as it was generated by the sequencer.
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145
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146 .. class:: warningmark
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147
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148
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149 @dataset_collections@
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150
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151 @description@
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152
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153 FASTQ=File
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154 F=File Output fastq file (single-end fastq or, if paired, first end of the pair fastq).
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155 Required.
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156
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157 SECOND_END_FASTQ=File
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158 F2=File Output fastq file (if paired, second end of the pair fastq). Default value: null.
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159
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160
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161 UNPAIRED_FASTQ=File
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162 FU=File Output fastq file for unpaired reads; may only be provided in paired-fastq mode Default
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163 value: null.
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164
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165 RE_REVERSE=Boolean
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166 RC=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them
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167 to fastq Default value: true. Possible values: {true, false}
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168
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169 INTERLEAVE=Boolean
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170 INTER=Boolean Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe
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171 which end it came from Default value: false. Possible values: {true, false}
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172
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173 INCLUDE_NON_PF_READS=Boolean
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174 NON_PF=Boolean Include non-PF reads from the SAM file into the output FASTQ files. PF means 'passes
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175 filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads.
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176 Default value: false. Possible values: {true, false}
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177
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178 CLIPPING_ATTRIBUTE=String
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179 CLIP_ATTR=String The attribute that stores the position at which the SAM record should be clipped Default
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180 value: null.
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181
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182 CLIPPING_ACTION=String
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183 CLIP_ACT=String The action that should be taken with clipped reads: 'X' means the reads and qualities
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184 should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in
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185 the clipped region; and any integer means that the base qualities should be set to that
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186 value in the clipped region. Default value: null.
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187
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188 READ1_TRIM=Integer
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189 R1_TRIM=Integer The number of bases to trim from the beginning of read 1. Default value: 0.
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190
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191 READ1_MAX_BASES_TO_WRITE=Integer
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192 R1_MAX_BASES=Integer The maximum number of bases to write from read 1 after trimming. If there are fewer than
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193 this many bases left after trimming, all will be written. If this value is null then all
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194 bases left after trimming will be written. Default value: null.
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195
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196 READ2_TRIM=Integer
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197 R2_TRIM=Integer The number of bases to trim from the beginning of read 2. Default value: 0.
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198
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199 READ2_MAX_BASES_TO_WRITE=Integer
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200 R2_MAX_BASES=Integer The maximum number of bases to write from read 2 after trimming. If there are fewer than
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201 this many bases left after trimming, all will be written. If this value is null then all
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202 bases left after trimming will be written. Default value: null.
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203
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204 INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean
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205 If true, include non-primary alignments in the output. Support of non-primary alignments
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206 in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and
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207 there are paired reads with non-primary alignments. Default value: false.
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208 Possible values: {true, false}
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209
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210 @more_info@
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211
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212 </help>
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213 <expand macro="citations"/>
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214 </tool>